Anchored in Armenia: An Exercise in Genetic Relativity [Original Work]

Introduction

Location of the Armenian Highlands in West Asia

As is the case with many groups in the region, the Armenians are, anthropologically-speaking, a very unique modern ethnicity. Situated in the Armenian Highlands (an expansive area straddling between the Zagros & Caucasus range) with a settlement history dating since the Neolithic, the modern Armenian people have maintained a distinct culture both shaped and shielded by the mountainous territory they inhabit. [1] One unique aspect of the Armenian people is their language; Modern Armenian is an Indo-European language belonging to its' own branch. There has long been scholarly debate regarding its' linguistic exodus from the Proto-Indo-European homeland (commonly accepted by modern linguists as the Pontic-Caspian steppe) [2] through to its' historical seat in the South Caucasus. As is evident by the attested Urartian and Hurrian loanwords in later forms of the language, Armenian must have been spoken by its' current forebears since at least before 500 B.C. [3] Various genetics enthusiasts (including myself) on differing occasions have cited this as an indication of an aboriginal West Asian genetic layer accompanying the Urartian-Hurrian vocabulary substratum.

Presumably due to the on-going political instability in West Asia, there has been an unfortunate lack of ancient DNA (aDNA) recovery in the areas adjacent to the Armenian Highlands. Alongside the Armenians, West Asia proper is also home to Anatolian Turks, numerous Kurdish groups, the Assyrians, several Jewish minorities and various ethnic groups within Iran. Inter-relation of all these groups in differing extents has been demonstrated in both published studies [4] and the open-source projects. [5,6]

Mount Ararat - A symbolic item in Armenian culture

Although they have most likely experienced their own demic events in prehistoric times, the insular nature of the Armenians relative to their neighbours allows them to be used as a stand-in for the aDNA we currently lack in this part of the world. In this blog entry, the Armenians will therefore be considered as a surrogate for autochthonous West Asian ancestry. They will be treated as a primary donor population (PDP) for several other West Asian groups, in an attempt to flesh out the degree of mutual shared ancestry, as well as the directions of added affinities beyond the region. This is by no means an authoritative attempt to purport a particular image of the West Asian genetic landscape, but an attempt instead to provoke discussion and explore the underlying structure of the region through a manner that should hopefully yield fruitful results in the glaring absence of aDNA in the region.


Working Hypotheses

1. Given the demonstrated similarity in autosomal DNA profiles (here and here), modern Armenians will serve as a reasonable PDP for all tested populations.

2. Furthermore, the genetic difference (GD) will likely be dictated by geographical proximity to the Armenians, or a (lack of) history of admixture with them.

3. Finally, the other donor populations will be anticipated either by virtue of geography or language.


Method

The Dodecad K12b Oracle was used to undertake this small project (please visit link for technical information). When executed through R, the program was set to Mixed Mode and fixed to 500 results for every iteration per population. The command entered therefore remained the same each time:

DodecadOracle("WestAsianPopulation",mixedmode=T,k=500)

Samples consist of nine location-specific populations (Iranians, Kurds_Y, Azerbaijan_Jews, Iraq_Jews, Iran_Jews, Turks, Turks_Aydin*, Turks_Kayseri*, Turks_Istanbul*) and four Dodecad participant averages (Iranian_D, Kurd_D, Assyrian_D, Turkish_D). A total of thirteen populations were therefore included.

From the output, only those combinations expressing an Armenian population as a PDP were selected. In this context, the Armenians will be considered a PDP if their "ancestral" percentage exceeds 50%. A maximum of ten were collected per population. In the event the number of combinations exceeded this, the subsequent combination lists are terminated with an ellipsis.

* Although not included in the original Dodecad K12b Oracle dataset, Dienekes has conveniently shared the population averages for these samples here. These were manually inserted into the command.

Results

Iranian and Kurdish Oracle results

Unsurprisingly, the Iranians and Kurds all display similar results. Specifically, the adoption of either Makrani or Balochi as the secondary donors when Armenians are fixed as a PDP. The proportions are also comparable between all. The Iranians appear to fit the Armenian + Balochi/Makrani combination slightly better than the Kurds (GD=4.04-5.16 vs. 5.03-6.65 to 2 d.p. respectively). It is also worth observing that both Iranians and Kurds, irrespective of sampling strategy (location-specific or Dodecad average), do not have Mixed Mode results which exceed ten.

Assyrian and select Near-Eastern Jewish Oracle results

The Assyrians are one of the groups of interest, given the demonstrated autosomal similarity between them and Armenians (here). As anticipated, their Mixed Mode results well exceed ten and the best fits (GD=1.66-1.82 to 2 d.p.) are all, coincidentally, with the Near-Eastern Jewish groups studied here. Subsequent matches include additional populations (e.g. Saudi, Bedouin, Syrian) where the GD remains relatively small compared to the Iranian and Kurdish values (>3.15 to 2 d.p.).

The Near-Eastern Jewish groups largely mirror the Assyrian results, although some key differences should be outlined:

• The Azerbaijani Jews have a GD similar to the Assyrians in range, setting them apart from the Iraqi and Iranian Jews. This seems to fit geography. However, if the association was strictly geographical, one would expect the Assyrians to lie in-between the Azerbaijani Jews from the Iraqi and Iranians. This may be genetic evidence of additional and direct ancestry between Armenians and Assyrians at some (or various) point(s) after the Near-Eastern Jewish groups had formalised their identities.
• Saudis appear as a secondary donor population in all groups. Interestingly, they appear to have an inverse relationship with geographic proximity to the Armenian Highlands; Iraqi, Iranian and Azerbaijani Jews are 20.4%, 16.1% and 7.8% "Saudi" respectively. The Assyrians too fall on this cline despite the point raised above.

Anatolian Turkish Oracle results

Finally, the Anatolian Turks provide us with another set of interesting values and pairs:

• Mixed Mode results from Western Turkey (Aydin, Istanbul) largely exhibit a combination of Armenian with various European ethnic groups or nationalities, which can be predominantly ascribed to geography. Please note the comparatively large GD among the Aydin average (>9.93 to 2 d.p.), which contrasts with Istanbul. I suspect the cosmopolitan nature of Istanbul has resulted in an artefactual lowering of the GD, given Anatolian Turks from
  across the country have moved their for employment purposes. [7]
• In contrast, the samples listed as "Turks" in Dodecad K12b (from the Behar et al. dataset, located in Central-South Turkey) model well as a combination of Armenian with either the Chuvash, Nogay, Uzbek or Uyghur. European secondary donors do make an appearance once more. Please also note their GD is the smallest out of the Turkish averages investigated (4.20 to 2 d.p.).
• The Kayseri average (Central Turkey) yielded no results matching the criteria outlined in "Method". However, the Assyrians instead made a frequent appearance as primary donors from GD=6.17 onwards. Given the genetic affinity between Assyrians and Armenians (refer above), and the consistency displayed by the Armenians as a PDP for other Turkish averages, this result can be considered anomalous. A close inspection of the Dodecad K12b proportions reveals the Kayseri Turks were on average approximately 1.5% more Southwest Asian than all other Turkish populations, explaining why Assyrians took preferential placing over Armenians as the PDP. The cause of this slight increase is unknown at present.
• The Turkish_D average best resembled that of Istanbul, albeit with slightly more Armenian and less European proportions. This would suggest that, overall, the Dodecad Turkish participants map somewhere just east of Istanbul despite the presumably diverse backgrounds. 
• Finally, all averages produced Mixed Mode results which exceeded ten in number.

IBD Segment Indications

To corroborate the findings of this investigation with additional genetic data, I refer to the Dodecad Project's fastIBD analysis of Italy/Balkans/Anatolia and fastIBD analysis of several Jewish and non-Jewish groups. As the analyses do not completely encompass those groups studied here, the results cannot be accepted wholesale. However, there does appear to be a broad agreement with some of the results in this investigation. For example, the Armenians and Assyrians have a demonstrated level of "warmth" to one another beyond background sharing.


Further Work

This investigation would have benefited from Azeri Turkish samples via the Republic of Azerbaijan. Additionally, a better breakdown of Kurdish, Iranian and Assyrian samples, akin to the site-specific sampling seen here in the Anatolian Turks, would have been ideal. Finally, as stated above, this investigation would have benefited from the inclusion of IBD segment analysis specific to the studied groups. Should time permit and the desired samples be made available in the future, this would be a natural line of inquiry to further what has been explored here.

Conclusion

Addressing the three hypotheses stated at the beginning in order:

1. Armenians certainly have behaved as a reasonable proxy for an autochthonous West Asian PDP in most of the populations tested (sole exception being the Kayseri Turks although this appears to be an anomalous response to slightly more Southwest Asian scores). The scores vary depending on the presence of the secondary donors, but Assyrians and Jewish populations from Azerbaijan, Iran and Iraq appear to have the largest proportion of this (occasionally surpassing 90%). All Iranians and Kurds, on the other hand, scored the least overall (approximately 65-75%). The Turkish range lies in-between these two.

2. Unfortunately, this isn't clear. The lack of regional results for Kurds and Iranians, together with a lack of samples specifically from Eastern Turkey, prevents any conclusion being reached on this point. The Near-Eastern Jewish populations studied here certainly do form a cline of Armenian "admixture" that is fully in line with geography. Furthermore, the large GD observed in Aydin Turks does support this idea, leading me to cautiously propose geography does indeed play a role. The second point also provides us with a partial answer, as the Assyrians demonstrate more of this than one would expect given their geographical placement based on GD, as well as fastIBD evidence from elsewhere.

3. With the exception of the Assyrians and Near-Eastern Jewish groups, the secondary donors overwhelmingly matched my expectations regarding their placement with whichever group that was studied (e.g. Iranians and Kurds towards South-Central Asia, Turks towards either Europe or Central Asia proper).

Over the coming years, with the availability of more data, we should hopefully move away from the population averages that have been used by various open-source projects. It has been empirically demonstrated here that regional results will differ significantly from nationwide averages (e.g. Aydin Turks vs. Turkish_D).

This also holds true on an individual basis; the best Oracle match for one Iranian via the described methodology was 56.4% Armenians_15_Y + 43.6% Tajiks_Y (GD=5.44 to 2 d.p.), differing significantly from both the Iranian and Kurdish averages.

I suspect the gentlemen running the numerous open-source projects are aware of this caveat and are, justifiably so in my opinion, making do with currently available data.

In closing, this investigation has also determined that, on the basis of the presumption of an Armenian-like autochthonous West Asian substrate, the studied populations as a whole have an apparent degree of inter-relatedness by virtue of this common South Caucasian autosomal heritage, albeit with the presence of highly significant affinities to elsewhere in Eurasia, be it population-wide, regional or even individual.


Speculations

The first topic is regarding the Iranians and Kurds; why were their average secondary donors always the Balochi's and Makrani, rather than more northern groups, such as the Tajiks? I suspect, when applied to population averages, the Oracle program effectively minimises intra-population variation to the point where only the broadest of affinities are indicated. In the case of Iranians, the secondary donor would therefore be one with genetic features that tend to emphasise the difference between Armenians and Iranians (e.g. additional South Asian and Gedrosian admixture). A similar conclusion can be reached with respect to the Turks.

Another interesting point is the demonstrated close relationship between the Assyrians and various Near-Eastern Jewish groups. This has been speculated upon in various discussion forums in the past. More precise tools will be required to elucidate whether these populations share legitimate ancestry with one another, or the affinity is happen-stance, instead reflecting the mixture of similar Near-Eastern groups with (again) similar Caucasus-derived groups at some point in history.

[Addendum I, 07/08/2014]: For a continuation on this with a fellow genome blogger, please read the Comments below.


Acknowledgements

Full credit for both the generation of raw population data and the Oracle program go to Dienekes Pontikos (Dodecad Ancestry Project).

Map of Armenian Highlands from Wikipedia.org. Photo of Mount Ararat courtesy of NoahsArkSearch.com.

Finally, I must refer all visitors interested in understanding the genetic constituency of the Armenian people to the FTDNA Armenian DNA Project. For a more interactive learning experience, two of the administrators (Mr.'s Simonian and Hrechdakian) recently delivered a lecture on this topic, garnishing it with a deeper description of anthropological and geographical aspects as described here.


References

1. Samuelian TJ. Armenian Origins: An Overview of Ancient and Modern Sources and Theories. [Last Accessed 3/08/2014]: http://www.arak29.am/PDF_PPT/origins_2004.pdf

2. Clackson J. Indo-European Linguistics: An Introduction. Cambridge Textbooks in Linguistics [Last Accessed 4/08/2014]: http://caio.ueberalles.net/Indo-European-Linguistics-Introduction/Indo-European%20Linguistics%20-%20James%20Clackson.pdf

3. Greppin JAC. The Urartian Substratum in Armenian. [Last Accessed 4/08/2014]: http://science.org.ge/2-2/Grepin.pdf

4. Grugni V, Battaglia V, Hooshiar Kashani B, Parolo S, Al-Zahery N et al. Ancient migratory events in the Middle East: new clues from the Y-chromosome variation of modern Iranians. PLoS One. 2012;7(7):e41252.

5. Dodecad Ancestry Project: ChromoPainter/fineSTRUCTURE Analysis of Balkans/West Asia [Last Accessed 4/08/2014]: http://dodecad.blogspot.com/2012/02/chromopainterfinestructure-analysis-of.html

6. Eurogenes Genetic Ancestry Project: Updated Eurogenes K13 and K15 population averages [Last Accessed 4/08/2014]: http://bga101.blogspot.com/2014/03/updated-eurogenes-k13-and-k15.html

7. Filiztekin A, Gokhan A. The Determinants of Internal Migration In Turkey. [Last Accessed 05/08/2014]: http://research.sabanciuniv.edu/11336/1/749.pdf

Worldwide Distribution of Dodecad K10a Components [Review]

Numerous ADMIXTURE runs have been completed by the Dodecad Ancestry Project since its' inception approximately two years ago. The status of certain components remained tenuous despite subsequent runs, whilst others provided fairly stable values for the bulk of the project's participants.

With the completion of the latest K10a run, I have composed a series of geographically accurate frequency maps with the intention of effectively presenting the trends that can be seen through the raw data.

Method

Data; values from over 130 groups obtained through the Dodecad K10a Spreadsheet. Only groups with at least 5 participants considered. Composites of populations were taken where appropriate and denoted with _cmp. Labels shown otherwise identical to source. The O_Italian_D group was excluded because no information on their origins were found online. 

Mapping; Dodecad participant populations allocated to national capitals. Exact location of reference populations obtained where possible (see Citations) however some allowances were made regarding those accompanied by scant information. Refer to the Data Sink for the population list, coordinates and commentary made during mapping process. No numerical data, aside from those shown for certain populations, was shown to minimise clutter and to remain faithful to the intention of this entry.

Population depiction; I deemed it necessary to separately consider the genetic structure of Jewish, Indian and expatriate/New World populations and exclude them from the rest of Europe, Asia or Africa. Including Jewish minorities with their gentile compatriots would render the maps uninformative. The complexity of India's demographics, particularly because of the caste system, makes frequency maps an improper choice for revealing inter-group genetic differences. 

Results

Acknowledgement

The raw values used in this investigation are attributed to Dienekes Pontikos, author of the Dodecad Ancestry Project.


Addenum I [04/07/2012]: Inclusion of All Components Colourised map, shown below:

Citations

http://www.uvm.edu/~rsingle/stat295/F05/papers/Cavalli-Sforza-NRG-2005_Ceph-HGDP-CDP.pdf
http://www.1000genomes.org/about 

http://www.sanger.ac.uk/resources/downloads/human/hapmap3.html  
http://alfred.med.yale.edu/alfred/recordinfo.asp?condition=populations.pop_uid='PO000019K
http://genome.cshlp.org/content/19/11/2154.full
http://upload.wikimedia.org/wikipedia/commons/b/b0/Caucasus-ethnic_en.svg

Autosomal variation from Anatolia to the Tarim periphery [Original Work]

The nature of ADMIXTURE as a tool for inferring ancestral components makes it difficult to discern the nature of a shared Autosomal component between several populations. For instance, a given component may originate in one population and be donated to others (e.g. purported African admixture in the Arabian Peninsula), stem from a mutual population (e.g. West Eurasian-specific components in low K=n runs between the Druze and the French Basque) or be the result of genetic drift (e.g. potentially, the peaking of East Asian-specific components in Korea and Japan).

Nevertheless, using results from the latest Dodecad Ancestry Project K12b run (link), I have investigated the component variation across a horizontal axis from Anatolia to the Tarim periphery in West China, with the intention of establishing the nature of the observed components across this area of interest. Raw values can be viewed on the newly-published Vaêdhya Data Sink. Populations are listed in a geographical cline.


One of the most immediate observations is the similarity between Kurdish and Iranian populations, with both expressing similar admixture percentages (deviation per component usually not >1%). This suggests that Kurds and Iranians have common origins, with the former largely maintaining those ancestral signals despite moving further westwards relative to their linguistic cousins in Iran.

Near-congruency between the Assyrians and Armenians is also striking, bar the variations on the North European, Caucasus and Southwest Asian components. It is again tempting to postulate the two descend for the most part from a similar root population with the aforementioned component differences accounting for the linguistic differences.

If one allocates the Kurds alongside the Iranians, several of the Autosomal components shown here have a distribution that appears to be determined by geography alone;

• South Asian peaks in Tajiks, who are situated approximately due NNW of the Indian Subcontinent.
  
• Caucasus reaches a maximum in Armenians and adjacent populations.
  
• Atlantic Med steadily decreases as one moves further away from Europe.
  
• Southeast Asian has an inverse relationship to the above, peaking in the Uyghurs sigificantly only.

Other components appear to have more complicated distributions;

• Interestingly, East Asian and Siberian are not too dissimilar in the populations containing them. The elevation of both in populations which speak Turkic/Altaic languages relative to neighbours speaking other languages confirms genetic input from the Turkish steppe nomads who expanded from the eastern side of Central Asia, eventually reaching the Iranian plateau and Anatolia. However, it is possible some of the Siberian and East Asian values may simply be the result of prehistoric demic diffusion across Eurasia (demonstrated by potential gradient between Kurds/Iranians <-> Tajiks), although this may in itself be of medieval steppe ancestry.
  
• Southwest Asian peaks in Assyrians, the only Semitic-speaking population shown in this analysis. This component falls rapidly beyond the Iranian plateau but is found at a background frequency east of Turkmenistan. Whether this is again an artefact of prehistoric demic movements or more recent migrations (e.g. Silk Road, various Persian empires) is debatable. As with the Siberian and East Asian components, there is an elevation which defies a geographical pattern and confirms historical accounts; the Tajiks, who descend in part from Persian speakers escaping Iran after the Sassanid collapse, show an elevation relative to the Uzbeks and Uyghurs. The greater frequency in Christian Armenians relative to the predominantly Muslim Kurdish territories and Iran disregards outright the notion it was introduced by the Islamic expansion out of the Arabian Peninsula.
  
• The Gedrosia component has a bifurcated peak between Iranians and Tajiks, implying an ultimate peak in the region of Pakistan (corroborated by other Dodecad population results, such as the Balochis of Pakistan). However, the Gedrosian frequency drops from a stable 28% across West Iranic-speaking populations to 13-18% in Anatolian Turks, Armenians and Assyrians. It is again impossible to infer whether this is of prehistoric origins (i.e. mutual Neolithic phenomena between the Iranian plateau and South-Central Asia) or more recent (inflated Gedrosian values a function of Median, Persian and Parthian ancestry).
  
• The North European component has what appears to be a dual geographic and linguistically-oriented distribution, which may be confounded further by recent interactions between Europe and some of the populations shown here (Anatolian Turks may potentially be the greatest example of this). It is interesting to note the Assyrian and Armenians show an inverse in the North European and Southwest Asian components despite otherwise appearing identical. The elevated frequency of this component in Central Asia will hopefully be covered in a future entry.

Despite the usefulness of ADMIXTURE in determining approximate ancestral origins of populations and individuals, it is impossible to ascertain the nature of component X between populations A and B; such Autosomal results should ideally be complementary to historical, linguistic, archaeological and even deep paternal and maternal evidence (Y-DNA, mtDNA).

Some of the observations made in this entry have been gleaned with earlier renditions of population data; through the use of deeper penetrating Autosomal techniques (such as IBD), the exact nature of the component variations should hopefully be resolved in the future.


Reference

The raw values used in this investigation are attributed to Dienekes Pontikos, author of the Dodecad Ancestry Project.