Tuesday, July 28, 2015

Comparison of Online Y-STR Predictors (Petrejcíková et al.) [◊]

An interesting study was published in 2014 based on Slovak Y-STR samples testing for 12 microsatellite markers. The main scope of this paper appears to be the investigation of the efficacy of three publicly available Y-STR haplogroup predictors (Athey, Cullen and YPredictor in alphabetical order) based on these 12 Y-STRs. Study contents shown below.

Y-SNP analysis versus Y-haplogroup predictor in the Slovak population.
Petrejcíková E, Carnogurská J, Hronská D, Bernasovská J, Boronová I, Gabriková D, Bôziková A, Maceková S. Anthropol Anz. 2014;71(3):275-85.
Human Y-chromosome haplogroups are important markers used mainly in population genetic studies. The haplogroups are defined by several SNPs according to the phylogeny and international nomenclature. The alternative method to estimate the Y-chromosome haplogroups is to predict Y-chromosome haplotypes from a set of Y-STR markers using software for Y-haplogroup prediction. The purpose of this study was to compare the accuracy of three types of Y-haplogroup prediction software and to determine the structure of Slovak population revealed by the Y-chromosome haplogroups. We used a sample of 166 Slovak males in which 12 Y-STR markers were genotyped in our previous study. These results were analyzed by three different software products that predict Y-haplogroups. To estimate the accuracy of these prediction software, Y-haplogroups were determined in the same sample by genotyping Y-chromosome SNPs. Haplogroups were correctly predicted in 98.80% (Whit Athey's Haplogroup Predictor), 97.59% (Jim Cullen's Haplogroup Predictor) and 98.19% (YPredictor by Vadim Urasin 1.5.0) of individuals. The occurrence of errors in Y-chromosome haplogroup prediction suggests that the validation using SNP analysis is appropriate when high accuracy is required. The results of SNP based haplotype determination indicate that 39.15% of the Slovak population belongs to R1a-M198 lineage, which is one of the main European lineages.
[Abstract] [Direct Link]

Are They Really Comparable?
Although all three predictors returned similar efficacy rates (~97-99%), it should be noted the authors' chief divisions of interest appear to be the conventional subclade designations currently used in both literature and the genetic genealogy community (e.g. R1a1a-M198). The authors correctly state Y-SNP testing is paramount in definitively gauging subclade classifications, especially for lines substantially downstream of a given haplogroup's phylogeny.

The rest of this entry determines whether these calculators display any other features which may give aspiring researchers reasons to choose one over another.

Subclade Coverage
A substantial difference is observed between the three. Athey's output is oriented around 21 categories spread across most of the major clades/subclades, although haplogroups not commonly found in West Eurasia (e.g. A-D) are unrepresented. Cullen improves on this significantly with 86 subclades, with Y-DNA I receiving the most attention (R1b to a lesser extent), with some improvements, such as well as the inclusion of "A&B". YPredictor has the highest count, hosting over 100 subclades, with the majority found in Y-DNA haplogroups E, G, J, N and R. With the exception of Y-DNA M and S, all are accounted for here.

STR count
Athey is capable of handling 111 Y-STR's (21 and 27-STR versions also available) with the format being listed in either numerical or Family Tree DNA (FTDNA) order. Cullen accepts a maximum of 67 STR's. YPredictor houses approximately 82 STR's. As such, all three are capable of handling a considerable number.

All three predictors permit the use of batched data and provide different means of categorising the data as seen fit by the user. Instructions are adequately provided for all three as well. As a research utility, however, YPredictor stands out through its' custom YFiler iterations (widely-used format in population genetics publications concerning Y-STRs) and debug feedback before predictions are made by the calculator.

Computational Time
This varies based on the user's CPU processing time, as well as whether they are manually entering STR values or inserting batched data. As such, this probably shouldn't be a pertinent factor in deciding which calculator to use.

Output Information
All three produce similar information (subclade prediction with probability expressed as a percentage).

Before summarising these findings, it is worth noting that Athey's predictor precedes Cullen's and YPredictor. As such, any perceived deficiencies in subclade breakdown or functionality are likely a result of age. Athey's predictor was widely used in the past, irrespective of the current application rate.

All three predictors are of use to genetic genealogists. This entry concludes the following "idealised" purposes for each:

  • Athey - For users keen to utilise upwards of 111 FTDNA Y-STR's as cross-validation against the other two
  • Cullen - Best for those seeking refined Y-DNA I or R1b subclade predictions
  • YPredictor - Most versatile and research-friendly, best worldwide coverage of Y-DNA subclades

As such, the three calculators certainly are comparable for making basic Y-STR predictions for West Eurasians, but obvious differences exist with respect to non-West Eurasian subclade coverage.

If compelled to make a single choice, I would recommend Cullen first to genetic genealogists of Northwest European paternal heritage (given the high frequencies of Y-DNA's I and R1b). YPredictor would be the best choice for those belonging to subclades more common outside Europe. This also explains why it has been extensively used in this blog to date. Athey's function has otherwise been usurped by the other two. 

Thursday, July 9, 2015

Presenting Bakhtiari Uniparental Marker Data [ƥ]

Bakhtiari people (Google Search)
The Bakhtiari people are one of Iran's ethnic minorities. Inhabiting the Iranian plateau's southwestern portion, the Bakhtiari traditionally maintained a hierarchical social structure with a genealogical basis (with organisations or positions including rish safids, kalantars, khans and ilkhani) [1]. Historically, the Bakhtiari have played a role in several pivotal events leading up to the formation of the modern Iranian state [2].

In recent years, the Bakhtiaris have received additional attention in the literature with respect to ancestry. This has been achieved predominantly via uniparental markers (Y-DNA and mtDNA) and coincides with work addressing the genetic origins of other ethnic minorities in Iran. For instance, in 2012, Grugni et al. expanded our understanding of Iranian Y-DNA across the country through sampling almost 1,000 unrelated men across 15 distinct ethnic groups (previous entry).

In spite of such developments, however, the Bakhtiari have not received much attention in either the genetic genealogy community or the literature. This entry attempts to explore the available data and arrive at a stable set of results for this group.

Khuzestan province, Iran (Wikipedia)

Search engines were limited to PubMed and Google Translate. Search terms included "Bakhtiari", "Y-DNA", "Y-Chromosome", "mtDNA", "mitochondrial", "STR", "SNP", "HVR" and "Iran". No limit was placed on publication date. All mtDNA and Y-DNA data was compiled. Where Y-STRs are presented, these were run through Vadim Urasin's YPredictor (v1.0.3 offline version). A 70% prediction strength threshold was implemented. If the resulting data is sparse, novel ways of consolidating the information will have to be devised and explained during the course of this entry.

Search Outcomes
Three studies were found to contain Bakhtiari uniparental data, with one partially covering Bakhtiari mtDNA (Derenko et al. 2013 [3]) and two for Y-DNA (Nasidze et al. 2008 [4], Roewer et al. 2009 [5]). The Bakhtiari populations featured mostly reside in Izeh, Khuzestan province, Iran [3-5] with a single sample coming from Lurestan province, Iran [4].

mtDNA Results
Derenko et al. featured only two Bakhtiari samples. One belonged to mtDNA H*, which was also observed in several Persian (Kerman province) and Qashqai samples, alongside a single Armenian. [3] The only other sample was mtDNA U2d2, also found in a single Persian (Kerman province). The authors noted that the combined frequency of mtDNA's U2c and U2d in Iran were highest among the Persians nationwide (approaching 10%) [3]. However, given the absence of additional samples, no reasonable conclusions can be drawn from these results.

Nasidze et al. provides both frequency and HVR1 derived variance data on the Bakhtiari and Ahwazi Arab populations [4]. The Bakhtiari appear to chiefly belong to mtDNA haplogroups N, U, H, T and J (below).

mtDNA Frequency Data from Khuzestan province, Iran {Nasidze et al. 2008)

Unfortunately, further information on subclade breakdown is not provided. However, as concluded by the authors and is evident through frequency data, the mtDNA profile of the Bakhtiari is almost identical to the Ahwazi Arab sample. Additionally, Nasidze et al. note "considerable sharing of HV[R]1 sequences" between these two groups [4]. In tandem with the inferences described above through Derenko et al., it appears that significant matrilineal marker overlap does exists across the Iranian plateau.

Y-DNA Results
Nasidze et al. first published data on 53 unrelated Bakhtiari men [4]. Due to substandard Y-SNP genotyping, the only conclusions that may broadly be discerned is the Bakhtiari chiefly belong to Y-DNA haplogroups J2-M172 (25%) and G-M201 (15%) (Data Sink). In this respect, these results cannot give observers a reliable indication of the Bakhtiari Y-DNA profile. Roewer et al.'s data indicates that some number of Bakhtiari do share the same core 17 STR haplotypes among one another (e.g. J2a4, T*)  but do not with any other samples across the country [5].

One "quick and dirty" way of addressing this problem is by using the YFiler (17 STR) Bakhtiari haplotypes (Data Sink) from Roewer et al. to "recharacterise" the Nasidze data. This is deemed the most suitable option for two reasons:
1) Nasidze et al. has an adequate sample size (n=53) but inadequate Y-SNP genotype selection
2) Roewer et al. has an inadequate sample size (n=18) and no confirmed Y-SNP testing, but the YPredictor data should provide reasonable subclade determination with a 70% probability threshold in place

"Recharacterisation" is achieved by expressing the Nasidze et al. data by the predicted subclade information provided by the Roewer et al. SNP predictions proportionally. For example, Nasidze et al. found "DE-YAP" at 8%, with the Roewer et al. predicted results showing 5.6% each for "DE*" and "E1b1b1". As both these subclades are contained within the DE-YAP node, the original value is recharacterised as DE 4% and E1b1b1 4%. The outcome is presented numerically (Data Sink) and demonstrated below (values rounded down to fit to 100%):

Y-DNA J2a4 constitutes the largest subclade (22.1%), with H (10.8%), R1a1a (8.9%) and T* (8.5%) following. The results imply considerable Y-SNP diversity within the Izeh Bakhtiari.

These results are somewhat at odds with that suggested by the Roewer et al. figures, particularly the frequency of Y-DNA J2-M172 (50% in Roewer et al. vs. 25% in Nasidze et al.). The most likely basis for this is sampling bias, given the former only tested for 18 individuals. It should be noted that Y-DNA J-12f2 has been documented to have a major (>60%) presence in Southwestern Iran (Quintana-Murci et al. 2001) with the majority of this likely being represented by downstream J2-M172 subclades (as per Grugni et al. 2012). It is therefore plausible for some Bakhtiari groups to yield exceptionally high frequencies of Y-DNA J2-M172 (likely J2a4 subclade) with future testing. The breakdown shown above is also broadly in line with past data from Southwestern Iran (Grugni et al. 2012).

It must be cautioned that literal interpretation of these results (both subclade breakdown and numbers) are not advised due to the inaccuracies brought by the "recharacterisation" and the lack of Y-SNP confirmation in Roewer et al.

It should also be emphasised that, as a tribal group, the Bakhtiari have most likely undergone genetic drift in their uniparental markers over time. As such, the finding of ~10% Y-DNA H is not completely surprising. Whether these values will be substantiated in future work is an open question.

The current evidence does suggest that the Bakhtiari closely resemble and share heritage with their immediate neighbours matrilineally, resting upon a backdrop of some common mtDNA diversity across the Iranian plateau. Inferences beyond this point will fall towards the realm of speculation.

The situation appears somewhat inverted on the Y-DNA side, where non-existent Y-STR haplotype sharing is observed with other groups in the Iranian plateau. The "recharacterised" data gives us an approximate idea of what the Bakhtiari Y-DNA profile should look like if Nasidze et al. used a better Y-SNP genotype panel.

Other ethnic minorities in Iran have received consistent attention in this respect, such as the neighbouring Qashqai and Lurs (Farjadian et al. 2011). The paucity in Bakhtiari uniparental marker data indicates this is very much an area that needs immediate attention. An initial first direction for researchers is to sample at least 50 unrelated individuals from Izeh using a more conventional Y-SNP genotype panel. Additional clarity will be gained by testing further areas, as well as reconciling the Bakhtiari tribal structure with these outcomes.

A very special thanks to the user "J Man" from Anthrogenica for bringing this interesting topic to my attention.

[Edit 10/07/2015]: I have also learned while researching this topic that Dr. Ivan Nasidze unfortunately passed away in 2012. His work served as an important early foundation towards understanding the genetic constitution of Caucasian and Iranian populations. May he rest in peace.

1. Bakhtiari. Last Accessed 25/06/2015: http://www.everyculture.com/Africa-Middle-East/Bakhtiari.html

2. Study of the Qajar government policy at the case of Household Bakhtiari. Last Accessed 6/07/2015: http://waliaj.com/wp-content/2014/Issue%201,%202014/26%202014-30-1-pp.124-127.pdf 

3. Derenko M, Malyarchuk B, Bahmanimehr A, Denisova G, Perkova M, Farjadian S. Complete mitochondrial DNA diversity in Iranians. PLoS One. 2013 Nov 14;8(11):e80673. doi: 10.1371/journal.pone.0080673. eCollection 2013.

4. Nasidze I, Quinque D, Rahmani M, Alemohamad SA, Stoneking M. Close genetic relationship between Semitic-speaking and Indo-European-speaking groups in Iran. Ann Hum Genet. 2008 Mar;72(Pt 2):241-52. doi: 10.1111/j.1469-1809.2007.00413.x. Epub 2008 Jan 20.

5. Roewer L, Willuweit S, Stoneking M, Nasidze I. A Y-STR database of Iranian and Azerbaijanian minority populations. Forensic Sci Int Genet. 2009 Dec;4(1):e53-5. doi: 10.1016/j.fsigen.2009.05.002. Epub 2009 Jun 5.

Friday, September 5, 2014

Worldwide Population Y-DNA Collated (Xu et al.) [◊∆]

Approximately one week has passed since a new paper by Xu et al. was indexed by PubMed and made available online ahead of printing:

"The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies."

This paper showcases a staggering 979 distinct Y-DNA 17 STR haplotypes across 44 distinct populations from across the world. These haplotypes are soon to be uploaded to the Y-STR Haplotype Resource Database (YHRD). The authors have made all the haplotypes, together with a slew of additional information, publicly available independent of the official article (raw haplotypes, Y-DNA haplogroup predictions).

In this entry, the collated results of all populations are reviewed, together with cursory inferences provided with the intention of aiding interpreting them.

All 979 haplotypes were retrieved through the above link. Each population dataset was run through Vadim Urasin's YPredictor (v1.5.0). A 70% prediction strength threshold was implemented. All nomenclature were reduced to the haplogroup level to avoid confusion for future readers should these change in time. These haplotypes formed the collated population results.

877 haplotype predictions met the 70% threshold established. Without having access to the original study, it is apparent that the authors also used Urasin's YPredictor, given the identical predictions.

The collated population results have been organised by the location of sampling by continent or region and can be found in the Data Sink. Direct links to each section accompanied by the list of populations sampled are listed below for the reader's convenience with a brief runthrough of some interesting findings under each.

1. Europe Adygei (Russia), Chuvash (Russia), Danes (Denmark), Finns (Finland), Hungarians (Hungary), Irish (Ireland), Khanty (Russia), Komi (Russia), Russians (Archangelsk), Russians (Vologda), Yakut (Russia)

The Adygei present as expected; they are predominantly G-P15 and J-L26 with various subclades of haplogroup R. Various subclades of haplogroups N and R define the Chuvash, with an additional appearance by J-L26 and Q-MEH2. Ethnic Russian populations appear to have their own regionalised diversity on the backdrop of being predominantly R-M198 and downstream subclades (particularly R-M458). The Irish are predominantly (~81%) R-M269, although the presence of a single man with H-M82 is surprising. Finally, the Yakut too belong overwhelmingly to haplogroup N (~78%) with a single man being predicted as I-P37.2.

2. Middle-East Druze (Israel), Samaritans (Israel), Yemenite Jews (Yemen)

The Druze are one of the better-sampled populations in this study, where they are mostly represented by various subclades of haplogroups E and G, together with R-M269 and T-L162. The Samaritans are defined (in order of decreasing frequency) exclusively by J-L26, J-P58 and E-V22. Finally, the Yemenite Jews present with a similar (though more restricted) spectrum as the Druze with some differences in frequency.

3. East Asia Ami (Taiwan), Atayal (Taiwan), Cambodians (Cambodia), Chinese (USA), Chinese (Taiwan), Hakka (Taiwan), Japanese (USA), Koreans (S. Korea), Laotians (Laos)

The Ami are unsurprisingly defined mostly by downstream subclades of haplogroup O, although there does appear to be an I-M223 and L-M317 among them. The Atayal, also of Taiwan, are exclusively O-MSY2.2. The Cambodians appear to have even more lineages which are typically expected further west. The Japanese boast the highest frequency of D-M55 out of all the populations sampled (21.1%). The Korean results contrast with this through the presence of men with N*-LLY22g(xM128,P43,Tat) and Q-MEH2. The Laotians appear to have one man with DE*-M1, although this will require SNP testing to definitively confirm.

4. Africa Ashkenazi Jews (S. Africa), Biaka Pygmies (CAR), Chagga's (Tanzania), Ethiopian Jews (Ethiopia), Hausa (Nigeria), Ibo (Nigeria), Masai (Tanzania-Kenya), Mbuti Pgymies (Congo R.), Sandawe (Tanzania), Yoruba (Nigeria)

The Ashkenazi Jews of South Africa appear to have a Y-DNA spectrum that is completely typical of Southwest Asians (please compare with the Druze). The Bagandu are largely defined by subclades of haplogroups B and E. Tanzanians here are completely haplogroup E and T. The presence of G-M15, J-L26 and R-M269 among the Hausa is surprising and may be attributed to a colonial European presence or some other forms of interaction.  The Sandawe have some rather unusual results given their geographical position (I-P37.2 and Q-MEH2), raising the possibility these haplotypes were predicted incorrectly.

5. Australasia Micronesians (Micronesia), Nasioi Melanesians (Solomon Islands)

Both the Micronesians and Melanesians have an unusually diverse spectrum. It is difficult to ascertain whether the parahaplogroups shown are genuine or, as described above, a result of incorrect predictions. A recent paper revealing the presence of newly discovered offshoots from haplogroup K in Southeast Asia [1] raise the possibility some of these may be genuine.

6. Americas Karitiana (Brazil), African Americans (USA), European Americans (USA), Maya (Mexico), Pima (USA), Rondonian Surui (Brazil), Ticuna (Brazil)

The Karitiana are predominantly Q-MEH2 but appear to have some non-American admixture through E-U175. African Americans are represented as an approximately 4:6 mix of R-M269 against various haplogroup E subclades. The Maya population, like the Karitiana, are Q-MEH2 with additional markers from outside the Americas, as are the Pima. The trend continues with the Quechua people, although C-M217 and T-L162 make their first appearance here. Finally, the Rondonian Surui and Ticuna are completely Q-MEH2.

There are at least two areas of the authors' methodology which are deemed to be drawbacks and prevent this study from being exceptionally informative.

Firstly, the authors evidently used the YFiler sampling array to complete this investigation. In an era where commercial testees can enjoy upwards of 111 Y-STR's, the long-term usefulness of this paper's extensive worldwide sampling is cut short. Another recent paper presenting Y-STR's worldwide has done so using 23 rather than just 17. [2]

My comments are more critical of the authors' sampling strategy. More data is never strictly a burden in the world of population genetics, but the informativeness of groups such as "European Americans", "Irish" and Chinese born in the USA is questionable. For instance, these groups are already richly represented, be it in the current literature or FTDNA Project groups. The apparent issue with these samples would have been rectified if they were simply obtained from a single area, providing regional specificity which may prove useful in better establishing genetic variation within Ireland, for example.

Finally, the haplotypes could have also received a "backbone" SNP test each to definitively place them within the current phylogeny. The drawbacks of STR-alone testing became readily apparent with some of the African samples. I can only speculate it is the highly divergent nature of certain uniquely African haplotypes from Eurasian ones which produced these spurious results.

On Mutation Rates (Quick Discussion)
In this study, both BATWING and the average squared distance (ASD) method were used. Within each, four different mutation rates were implemented. On initial inspection these appear to vary wildly. However, on closer examination, it appears all the BATWING most recent common ancestor (MRCA) calculated ages are approximately twice as old as those generated by the ASD method. Even within each technique there is substantial variation; the evolutionary rate appears approximately three times greater than the others. Furthermore, these "other" mutation rates do tend to congregate around a common similar value (e.g. through BATWING, the calculated global age of their Y-DNA R-M198 haplotypes was 5.5k, 6.1k and 6.2kya), which would intuitively suggest the "actual" value lies somewhere within these either through BATWING or ASD. The discrepancy here cannot be overstated and calls into question why some researchers are still utilising a "blanket" mutation rate across several loci which are shown to have significantly different tendencies to mutate (colloquially described as "slow", "medium" and "fast" mutators). I am uncertain whether the authors are in fact doing this, but the implications of this are apparent, as they prevent rational "fitting" of these numbers into candidate prehistoric narratives from happening. This entire topic will likely be explored in a future entry.

Although at least three drawbacks (four including the MRCA calculations) are identified here, this study provides researchers worldwide with a plethora of data from populations that are either poorly represented in the current literature or have been entirely absent until present. The majority of the results outline the wide Y-chromosomal diversity across the world, whilst also revealing specific trends that have been established in both the current literature and in online discussion boards. An mtDNA counterpart of this paper would be a wonderful addition to see sometime in the near future.

There is a bountiful amount of data to be interpreted with pre-existing ideas/models and compared with prior studies which place a premium on each population's area. I welcome any form of dialogue regarding the results. There, is, for many of us, plenty to elucidate. The conclusion does not end here; I encourage as much further investigation and thought by the readers as the data permits.

[Addendum @ 05/09/2014]: Error regarding Karitiana data. Modified and updated.

1. Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF. Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia. [Last Retrieved 03/09/2014]: http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2014106a.html 

2. Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R et al. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. [Last Retrieved 05/09/2014]: http://www.fsigenetics.com/article/S1872-4973%2814%2900084-2/abstract

Wednesday, August 6, 2014

Anchored in Armenia: An Exercise in Genetic Relativity [ƥ]


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.


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:


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.


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.


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.


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.


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.


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

Saturday, July 13, 2013

A Hidden Gem in Central Asia: Previously Unknown Y-DNA R1b Haplotype [◊∆•]

1. Introduction

Central Asian Y-DNA diversity has been an area of constant intrigue in the genetics community. Wells et
al.'s The Eurasian Heartland: A continental perspective on Y-chromosome diversity paved the way, with several others following in their regard. Members of the same team (including Dr. Wells) produced another paper - A Genetic Landscape Reshaped by Recent Events: Y-Chromosomal Insights into Central Asia - on the same topic in the following year, this time headed by Dr. Tatania Zerjal. I noted a greater emphasis on East-Central Asian populations as well as a mentioning of Y-STR analysis in the study itself. However, none of this data was supplied, with only Y-SNP information included (shown sporadically in this entry). The age of this paper is apparent through the nomenclature used (see Method section).

Several months ago, I made a request to obtain the Y-STR data from this study to one of the co-authors, Dr. Tyler-Smith, who kindly replied with the results of all sampled populations (Data Sink > Zerjal et al. Raw Data).

In this blog entry, the Y-STR data is showcased with a special emphasis on the Y-DNA R1b-M269 which was discovered.

2. Method
Y-SNP Phylogeny in original paper (Zerjal et al.) [1]

The maximum number of compatible Y-STR's were utilised for processing in Urasin's YPredictor for easier haplogroup identification (14 of a possible 16, DYS434 and 435 were excluded). All data was run through YPredictor. Only samples with ≥70% probability were included in the final results (Data Sink > Processed Data). As discussed below, relevant findings are compared with the basic Y-SNP haplogroups shown in the original study (on right).

One point which needs to be addressed immediately is the high frequency of "_DE-M1" and "P-M45". It appears that the STR selection has led to a phantom result, rendering many of the samples useless. For instance, the original study shows the Kazakhs belong overwhelmingly to C3c-M48, [1] although the probable results shown here are mostly "_DE-M1".  The exclusion of DYS434 and 435 from my level of processing likely contributed to this; if one assigns equal weight to the statistical strength of a prediction, removal of two STR's from a panel numbering 16, accuracy is reduced by 12.5%. Additionally, some conversion error seems to have applied with DYS437 (i.e. a value <12 is unusual). Therefore, "_DE-M1" and "P-M45" results were dismissed on account of the mismatch between predicted and likely confirmed haplogroups probably due to a compatibility issue between the study's STR panel and YPredictor..

3. Results

As the majority of samples were removed owing to the caveat described above, this entry will take a qualitative rather than quantitative approach to analysis on the general picture formed. Much of the remaining results are congruent with findings in other papers. Populations around the Caucasus are signified by plenty of R1b-M269, J2a-M410 and G2a-P15. Tajiks and the Kyrgyz were predominantly R1a1a-M17. Mongolians and other East-Central Asian ethnic groups yielded the most O3-M122 and "NO-M14" (likely to be Y-DNA N or O suffering from the STR restrictions described in the Method section).

Y-SNP distribution in Central Asia (Zerjal et al.) [1]

3i. The R1b Signal 

R1b-M269 was found across Central Asia and not only in the Caucasus (Armenians, Azeris, Georgians, Ossetians). It was mostly detected among the Turkmen (trk1, trk2, trk4, trk6, trk7, trk22, T29, T32) with a single sample among the Uzbek (uz-s110). [1]

Analysis of the haplotypes (including DYS434 and DYS435) revealed the nine Central Asian R1b samples belonged to a secure haplotype (Data Sink > R1b Results). trk6 diverged greatest, albeit with two 1-step mutations on DYS393 and DYS434. The rest match this haplotype exactly or have single 1-step mutations. [1] When this Central Asian R1b haplotype is compared with the other Caucasian samples, a mixed picture emerges, with the poorest being an Armenian (arm47) at 8/16, whereas the best are another Armenian (arm12) and Azeri (az48), both at 15/16. [1]
One interesting point is the Kurds sampled in this study (some of whom also belong to R1b-M269) are actually the displaced population positioned on the Iranian-Turkmenistani border. All of whom match the Central Asian R1b haplotype with a similar value (12-13/16). This definitively rules out the Kurds as a source for the haplotype, particularly as better matches can be found further to the west. It should be noted the Kurds themselves formed their own R1b haplotype (defined here by DYS389II=27, DYS391=10). [1]

In summary, the data reveals that the Turkmen are particularly abundant in R1b-M269 and all belong to the same haplotype as one of the Uzbek samples. This haplotype matched some Caucasians very well, but others not so well. The Kurds living in Turkmenistan belonged to their own haplotype.

3ii. Is This Actually R1b-M269?

Attention must first be shown to the original paper again; any potential R1b-M269 here will be present as P(xR1a)-92R7 (shown in the paper as "Haplogroup 1"). [1] Evidently, this makes up approximately half of the Turkmen lines and a quarter of Uzbek ones. Other haplogroups (such as other forms of R1b, R2a-M124, various Q subclades) presumably make up the rest of "Haplogroup 1" shown.

The next step is to verify whether or not this Central Asian R1b haplotype matches other R1b haplotypes online. As Y-DNA R1b-M269 is fortunately well-represented in the world of genetic genealogy, searching for the haplotype's matches on ySearch is a reasonable enterprise. DYS437 had to be excluded here due to a conversion issue, leaving the haplotype at 15 STR's. A genetic distance (GD) of 3 was allowed on these 15 markers. Results are shown on the right.

ySearch results for Central Asian R1b haplotype
With some confidence, the search has demonstrated that the Central Asian R1b haplotype does indeed belong to R1b-M269, as all the seven matches shown (one of whom is Armenian) belong to it.

Expanding the line of inquiry one further step came through comparing this haplotype with Iranian haplotypes [2] which were readily available. Due to differences in STR panels (an overlap of only 11) this proved to be inconclusive, aside from the observation that DYS389i+ii was completely different between the Central Asian modal (10-26) and the Iranian values. At this point I suspect that, much like DYS437, there is a conversion issue with DYS389 also.

Finally, a comparison was made with the R1b found in Afghanistan last year [3]. Interestingly, if DYS389i+ii and DYS437 are excluded, the two Uzbeks (samples 35 and 181) match the Central Asian R1b haplotype almost exactly based on the remaining 11 STR's. The one Tajik (sample 32) is less likely to be related due to two 1-step mutations on different STR's.

4. Conclusion

The inferences made from the data hang by a metaphorical thread due to the persistent STR issue; different labs have used different panels in the past decade, making it excruciatingly difficult to use materials from older papers. Fortunately, the presence of a specific strain of R1b-M269 in Central Asian (in Turkmen and Uzbeks) has successfully been demonstrated after select exclusions and no modifications to the data.

However, some larger questions remain. If STR limitations were not an issue, how would the Iranians from Haber et al. have compared? Would the Tajik from the other Haber et al. paper have belonged to the same haplotype in the end?

The origin of this Central Asian R1b haplotype will, I anticipate, also be a point discussed heavily among interested parties. At this point in time, I must stress that none of the evidence thus far points to anything in particular without ruling other theories out, although it leaves the door for interpretation wide open.

Having given this cautionary statement, the main thrust of this entry should be emphasised; R1b-M269 in Central Asia is a confirmed reality and here to stay. I will defer any subsequent analyses to the experts on Y-DNA R1b which grace several genetic genealogy boards for their take on the flavour of this haplotype.

5. Acknowledgement

I publicly extend my gratitude to Dr. Tyler-Smith for being so kind in sending me the raw STR's from this important paper for my research, as well as co-authoring the other two excellent studies I have cited here and in the past.

6. References

1. Zerjal T, Wells RS, Yuldasheva N, Ruzibakiev R, Tyler-Smith C. A genetic landscape reshaped by recent events: Y-chromosomal insights into central Asia. Am J Hum Genet. 2002 Sep;71(3):466-82. Epub 2002 Jul 17.

2. Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA. Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. Eur J Hum Genet. 2011 Mar;19(3):334-40. doi: 10.1038/ejhg.2010.177. Epub 2010 Dec 1.

3. Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, Martínez-Cruz B. Afghanistan's ethnic groups share a Y-chromosomal heritage structured by historical events. PLoS One. 2012;7(3):e34288. doi: 10.1371/journal.pone.0034288. Epub 2012 Mar 28.

Tuesday, March 26, 2013

Y-DNA Haplogroup N in India: Wayward Uralics or Lab Error? [◊∆•]

Y-DNA Haplogroup N Eurasian Distribution

Per ISOGG's 2013 SNP tree and as has been the case for years, Y-DNA Haplogroup N is defined by the M231 mutation (G->A at rs9341278) on the Y-Chromosome. With a predominantly North Eurasian distribution, it peaks in Europe among the Finnish people and various ethnic groups residing in Russia's far north through the N1c-Tat subclade. N1c-Tat specifically is frequently associated with Uralic-speaking populations in the literature.

Haplogroup N also appears to have an association with Central Asia as shown in the N Y-DNA Haplogroup Project (FTDNA) results, with several samples coming in from Kazakhstan, Uzbekistan and Mongolia. It has also been observed in Turkey (KurdishDNA blog entry) as well as appearing in 1.6% of Iran's Azeri population (Grugni et al. entry).

The finding of Haplogroup N in India through Sharma et al.'s The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system [1] is a curious one. Unfortunately, the paper did not include any Y-STR material to help understand the basis of N's presence in India.

Significance of Potential Haplogroup N in India

Linguistics provides us with a plausible scenario regarding how Haplogroup N may have arrived in the Indian Subcontinent. Contacts between early Finno-Ugric and Indo-Iranian groups took place around the Ural mountains, specifically between the forest and steppe zones. Evidence of transmission in horsekeeping techniques, economy, deities and common words are firmly established from Andronovo archaeological horizon on the steppes into the "Andronovoid" societies living in the nearby forests. [2]

The presence of Haplogroup N in India, if present in relevant populations and displaying MRCA values or STR clusters consistent with a Neolithic origin further north, would satisfy the likelihood of Haplogroup N representing an accompanying genetic signal from the steppe zone roughly four thousand years ago, as well as serving as a genetic remnant of the interactions that undoubtedly took place between Indo-Iranian and Finno-Ugric tribes.

Current Findings

In 2009, Sharma et al. published a paper highlighting the Y-Chromosome haplogroup differences between various upper caste (Brahmin) and tribal populations across India. The paper went on to deduce that Haplogroup R1a1a in India was autochthonous in origin based on their findings [1] (now disputable and improbable based on Underhill et al.'s landmark study on Y-DNA R1a1a and recent findings by the R1a Subclades FTDNA Project, although this topic is beyond the scope of this entry).

It was this very paper by Sharma et al. which revealed the presence of Y-DNA N in India. Haplogroup N1-LLY22g was found in Brahmins from Gujarat, Madhya Pradesh and Mahastra (3.13%, 2.38% and 3.33% respectively), as well as tribal populations from Uttar Pradesh (1.56%). Their results were extended to include greater caste differentiation (Brahmins vs. Scheduled Castes vs. Tribals); here, Brahmins were found to have five times greater the frequency of N1-LLY22g than tribal groups (0.5% vs. 0.1% respectively).  [1]

Although the frequencies were arguably insignificant, the inference stood - Y-DNA Haplogroup N showed an association with the upper caste practitioners of Hinduism in India, paving the way for the scenario described in the above chapter to be considered.

However, the strength of this conclusion is weakened greatly by cross-sectional data from numerous studies concerning the Indian Subcontinent produced in the past decade:

  • Sengupta et al. (2006) revealed that, out of 1090 samples, with the majority coming from the Indian Subcontinent, the only populations revealing any Haplogroup N (N-M231) and associated downstream subclades were either East Asian (Chinese ethnicities, Cambodian) or Siberian (Yakut). [3] No groups from India belonged to Haplogroup N-M231.
  • Furthermore, Sahoo et al. (2006) also sampled individuals from across the Indian Subcontinent (n=1074) and failed to find a single instance of N-M231. [4]
  • In a recent study on various populations in Tamil Nadu (South India), Haplogroup N was completely absent in the 1680 samples tested. [5]
  • Y-DNA N1c-Tat was absent in the 607 tribal populations tested from East and Northeast India. [6]
  • Returning to the north of the country, 560 men from various upper castes and Muslim groups were tested by Zhao et al. and N1c-Tat was absent from all. [7] 
  • Focused specifically on Brahmins from Saraswat (Jammu-Kashmir), Yadav et al. found none of the approximately 109 haplotypes to belong to any derivative of Haplogroup N. [8]

Finally, the N Y-DNA Haplogroup Project at FTDNA currently does not show any samples whatsoever from the Indian Subcontinent.

Possible Explanation

Despite over 4,000 samples over five studies representing various groups from across India, not a single trace of Haplogroup N has been detected. What explains this glaring discrepancy with Sharma et al.'s findings? Differences in sampling strategy between the other studies with Sharma et al. cannot account for this; there is enough regional overlap to rule this out.

As was the case with Sengupta et al. where several Hazara haplogroup classifications were allegedly due to a laboratory error, it is probable the Haplogroup N seen here follows the same suit. By reasonable deduction, if one study reveals a trend that several others covering thousands of samples cannot verify, there must be something intrinsically erroneous in the former.


Until I can physically view the purported Haplogroup N haplotypes reported in Sharma et al., it is the conclusion of this entry that they are most likely the result of a laboratory error given the complete absence of any flavour of N-M231 in India through other recent studies. If any Haplogroup N is found, it must be contrasted against Sharma et al. and should be investigated on a separate line of inquiry. As ever, details of any future cases of Haplogroup N in India should be taken into consideration. If of a Mughal background, the paternal origins are readily explained by Medieval Central Asian ancestry. If from the furthest northeast of the Indian Subcontinent, the possibility of Nepali ancestry should be sought. [9] Although prehistoric indirect influence from Finno-Ugric interactions in the second millennium BC onwards shouldn't be dismissed outright, other more recent explanations exist.


1. Sharma S, Rai E, Sharma P, Jena M, Singh S, Darvishi K. The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system. J Hum Genet. 2009 Jan;54(1):47-55. doi: 10.1038/jhg.2008.2. Epub 2009 Jan 9.

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

3. Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow CE. Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet. 2006 Feb;78(2):202-21. Epub 2005 Dec 16.

4. Sahoo S, Singh A, Himabindu G, Banerjee J, Sitalaximi T, Gaikwad S. A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios. Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):843-8. Epub 2006 Jan 13.

5. Arunkumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS. Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system. PLoS One. 2012;7(11):e50269. doi: 10.1371/journal.pone.0050269. Epub 2012 Nov 28.

6. Borkar M, Ahmad F, Khan F, Agrawal S. Paleolithic spread of Y-chromosomal lineage of tribes in eastern and northeastern India. Ann Hum Biol. 2011 Nov;38(6):736-46. doi: 10.3109/03014460.2011.617389. Epub 2011 Oct 6.

7. Zhao Z, Khan F, Borkar M, Herrera R, Agrawal S. Presence of three different paternal lineages among North Indians: a study of 560 Y chromosomes. Ann Hum Biol. 2009 Jan-Feb;36(1):46-59. doi: 10.1080/03014460802558522.

8. Yadav B, Raina A, Dogra TD. Genetic polymorphisms for 17 Y-chromosomal STR haplotypes in Jammu and Kashmir Saraswat Brahmin population. Leg Med (Tokyo). 2010 Sep;12(5):249-55. doi: 10.1016/j.legalmed.2010.05.003.

9. Gayden T, Chennakrishnaiah S, La Salvia J, Jimenez S, Regueiro M, Maloney T. Y-STR diversity in the Himalayas. Int J Legal Med. 2011 May;125(3):367-75. doi: 10.1007/s00414-010-0485-x. Epub 2010 Jul 21.

Saturday, December 22, 2012

Yaghnobi Tajiks: Preliminary Results May Reveal Iranian Plateau Affinity [◊∆•]

Slipping under the radar of the genetic genealogy world is this paper by Elisabetta Cilli and her colleagues, which investigated the mitochondrial data of 62 individuals from Tajikistan's Yaghnobi population. [1]

The Yaghnobis are of interest given their geographical isolation and the East Iranic nature of their language. Living just northeast of the predominantly Persian (Dari) speaking capital, Dushanbe, Yaghnobi is a continuation of a fully agglutinative Soghdian dialect representing the sole survivor of this language following the Persianization of Central Asia in Medieval times [2]. Despite its' East Iranic vocabulary, Yaghnobi demonstrates several linguistic features (i.e. gender loss, past imperfective preservation from present stem of a verb) which separates it from those modern East Iranic languages immediately surrounding it. Furthering the uniqueness of the Yaghnobi language in this context is the unity it forms through these features with languages mostly spoken further west in the Iranian plateau (e.g. Persian, Gilaki, Kurdish dialects). [2]

Although the results are preliminary and lack any empirical data, Cilli et al. have discovered some interesting connections between the Yaghnobi and relevant populations. In summary, they found the following:

MDS Plot of Results
  • 42 individuals used for the preliminary work belonged to only 19 distinct mtDNA haplotypes. Of these, 11 were distinct among the Yaghnobi.
  • The Yaghnobi have less mtDNA genetic diversity than other Central Asian populations (0.930) and this is attributed to their geographical isolation and recent history of displacement by the U.S.S.R. in the 1970's for agricultural purposes, where a small group (300) returned and repopulated their original homelands.
  • Intriguingly, the Yaghnobi shared all of the mutual haplotypes (8/19) with populations from Iran (e.g. Gilakis, Mazandaranis and Iranians from Tehran and Esfahan) instead of other Central Asian groups, including their Tajik compatriots.
  • The Yaghnobi shared most of these mutual haplotypes with Gilakis, Kurmanji Kurds and Avars from the Caucasus (4 each).
  • However, owing to their predominantly distinct mtDNA character, the Yaghnobi are clear outliers from the general zone occupied by the reference groups. 

My critique and interpretation of these results are as follows:

  • At least two instances of genetic drift occurring (founder effect via geographic isolation, bottleneck due to Soviet relocation) is likely responsible for the decreased mtDNA diversity. Thus, it is clearly simply a reflection of their environment.
  • As a result of the Soviet relocation, it may be useful to determine whether results from the displaced parent population match what has been stated here. This is quite possible given the relocations occurred just over one generation ago (~40 years).
  • It is difficult to criticise the decision to test 62 individuals and the utilisation of 42 haplotypes, given the Yaghnobi population in their homeland between 2007-9 only numbered approximately 500. Approximately 8% of the entire Yaghnobi population was therefore analysed here, which is a generous frequency given the amount of attention the region has received.
  • The MDS plot would have benefited from the inclusion of populations in Europe, Southwest Asia and South Asia to comprehensively flesh out the position of Yaghnobis in Eurasia.
  • Accepting that this is a preliminary investigation, it would still have been pleasing to see some raw data published. Aside from confirming that some/one Yaghnobi matched the Cambridge Reference Sequence (CRS, thus Haplogroup H2a2a which happened to be found in all the populations tested), there is no indication as to what the other mutations looked like. Or, for that matter, what mtDNA haplogroups were even present!

Correlation with Y-Chromosomal Data?

The Yaghnobi have been studied at least one other time through their inclusion in Dr. Spencer Wells et al.'s seminal piece The Eurasian heartland: a continental perspective on Y-chromosome diversity. The breakdown of their Y-Chromosomal SNP data (n=31) is as follows: [3]

3% C-M130(xC3a3-M48)
32% J2-M172
Y-SNP clustering reveals Yaghnobis sit near SE Europe and the Near-East
3% K-M9(xO-M175, O3-M122, O1a-M119, O2a1-M95, N1c1-M46) (possibly parahaplogroup such as K*-M9)
10% L-M20
3% P-M45 (xQ1a1-M120, Q1a3a1-M3, R2a-M124)
32% R1-M173 (likely R1b1a1-M73 or R1b1a2-M269)
16% R1a1a-M17(xR1a-M87, private marker)

Despite the double genetic drift undoubtedly affecting the frequencies, it is worth pointing out that the Yaghnobi presented with a broadly similar Y-DNA spectrum as Iran, where J2-M172, L-M20, R1-M173 and R1a1a-M17 (including subclades) comprise approximately 53% of the national average (refer to Grugni et al. analysis). 

This comparison should be taken with a grain of salt given the Iranian national average also comprises non-Iranic-speaking ethnic groups, the Wells Yaghnobi data does not present with thorough downstream Y-SNP evidence, the sample size is contentious and at least two contributors of a founder effect exist. However, that the Yaghnobi appear rich in J2, L and R is certainly reminiscent of Iranic-speaking populations in the region.


The Yaghnobi are an exceedingly interesting population whose overall parental markers seem to support a connection with populations further west than one would anticipate.

Despite the misgivings of all the data concerning them to date, the mtDNA similarity does corroborate specific linguistic features between the Yaghnobi language with those in the Iranian plateau, such as Kurdish or Persian.

If the data holds up in future investigations, it certainly calls to question whether the proposed model of linguistic inheritance exclusively down the parental line (as represented by Y-DNA data) is entirely correct given this connection.

How the Yaghnobi came to display the markers within them whilst speaking an East Iranic dialect with traits akin to those found in West Iranic languages is an intriguing question. One possible scenario is that the Yaghnobi are partly descended from ancient Iranians from the Iranian plateau during the Achaemanid era. This would also account for the linguistic commonalities noted in current literature.

Time (with the assistance of more mtDNA, Y-DNA and auDNA) will help us understand what happened in Central Asia during the formative period that was the Indo-Iranian migrations.


1. Cilli E, Delaini P, Costazza B, Giacomello L, Panaino A, Gruppioni G. Ethno-anthropological and genetic study of the Yaghnobis;an isolated community in Central Asia. A preliminary study. J Anthropol Sci. 2011;89:189-94.

2. Windfuhr, G. The Iranian Languages. 1st ed. Routledge Language Family Series. 2009.

3. Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, Blue-Smith J. The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc Natl Acad Sci U S A. 28;98:10244-9. 2001.

Sunday, August 19, 2012

Introducing the ACD Tool [ƥ]

It is with satisfaction I announce the release of my first ever population genetics spreadsheet for fellow researchers. The Ancestral Component Dissection (ACD) Tool is a piece freeware I have developed to give those with a similar knack for fiddling with ADMIXTURE, Y-SNP and mtDNA frequency data better means to flesh out inter-population differences.

ACDTool (v1.0)
How Does The ACD Tool Work?

The ACD Tool relies on the frequencies of "ancestral components", a general catch-all term for uniparental markers (Y-SNP's, mtDNA) and Autosomal DNA (auDNA). These form the mainstay of much of the work that has been done in population genetics for the past few decades. The advent of "genome blogger" projects has brought the immediacy of these techniques to those who have tested with personal genetics companies, such as Family Tree DNA (FTDNA) and 23andMe. The ACD Tool should therefore be considered a supplementary item by those interested in these results, as well as data procured from current literature.

The level of commonality that occurs between many populations and ethnic groups poses a problem for those interested in investigating what differences arise between them.

To solve this, the ACD Tool works by removing mutual shared component frequencies between sample averages within a region. The idea is to lessen the amount of regional similarity and intentionally exaggerate those differences that exist between neighbours.

This is achieved by removing congruent component values across all populations (using the lowest value as a benchmark), leaving only the differences behind.

What Experiments Are Ideal?

As the ACD Tool is intended for finer inter-population analysis, it is best applied in a regional context. It serves the purpose of better revealing genetic differences which may account for linguistic or micro-regional trends.

Example #1: Northeast Europeans (Dodecad)

Once the Polish, Russian and Finnish Dodecad cohort averages were run through the ACD Tool, I simply used Excel to create the charts. The "Before-After" feature is used to highlight that the tool has completely achieved its' desired goal in amplifying the genetic differences between them:

NE European auDNA (Dodecad) through the ACD Tool

Example #2: West Asians (Harappa)
Using the Harappa Ancestry Project this time, I ran the data of Armenians, Assyrians, Kurds and Iranians (mostly from the Harappa cohort) into the ACD Tool once more and presented the differences as above:

W Asian auDNA (Harappa) through the ACD Tool

Example #3: South-Central Asians (Eurogenes)
A final example pits Pathans, Jatts, the Burusho, Balochis and Brahuis against one another:

SC Asian auDNA (Eurogenes) through the ACD Tool

Are There Any Drawbacks?
The efficacy of the ACD Tool depends on the number of populations, cohort size and cohort specificity. As the examples above show, the level of inter-population component sharing may decrease greatly if groups that are from more genetically diverse regions are compared.

In addition, using the ACD Tool on populations that are too different (i.e. Han Chinese and Yoruba) will not work given the genetic overlap through either ADMIXTURE, Y-SNP's or mtDNA is negligible. Of course, this defeats the point of the tool in the first place.

Lastly, the tool requires Macros to be enabled for the instructions to work.


The ACD Tool is an open-source free-to-use spreadsheet. Those wishing to modify the spreadsheet for their personal use are welcome to do so. However, any modifications made to the ACD Tool with the intent of subsequent redistribution are kindly asked to contact the creator (myself) before doing so out of common courtesy.

Please also note the ACD Tool is a first attempt at giving back to the genealogy world I have been a part of for several years. Though functional (as shown above), it is not without bugs. In light of this, I am not responsible for any loss of data that may occur from its' use.

Finally, I hope the genealogy world finds some use for this nifty piece of kit.


To the Dodecad Ancestry ProjectHarappa Ancestry Project and Eurogenes Genetic Ancestry Project (auDNA used in Examples).

Addentum I [20/08/2012]: ACDTool v1.1 replaces v1.0, Macros smoothened and instructions refined. Eurogenes South-Central Asian example also added.

Saturday, August 4, 2012

West Asian Y-DNA Haplogroup Q - Turkish or Autochthonous Origins? [ƥ]

Genographic Project Y-DNA Q Migration Route

Y-DNA Haplogroup Q is defined by the M242 marker and is upstream to Haplogroup P-M45, making it the sister Haplogroup of R-M207, which populates much of West Eurasia. According to the Genographic Project, Haplogroup Q-M242 is between 15-20,000 years old, with the location invariably being placed around North Eurasia.

The frequency of Haplogroup Q largely matches the migration path outlined in the maps shown opposite. However, the presence of haplogroup Q in more southwestern portions of Asia has sparked the curiosity of genealogists and observers alike. In current literature, the presence of Haplogroup Q1a2-M25 specifically in Iran is cited as "Central Asian" influence. [1]

In an attempt to conclusively uncover the origins of Haplogroup Q-M242 in West Asia, the Y-STR haplotype variation of West, Central and South Asian Q1a-MEH2 and Q1b-M378 are visualised and analysed with genealogical tools.

The data for this investigation are gathered from various Family Tree DNA (FTDNA) projects and studies, [1,2,6-11] with the concise list shown in the References section below.

Only results presenting at least 16 Y-STR's were considered. Modifications were made as necessary on certain STR markers (particularly Y-GATA H4) to correct nomenclature differences. Urasin's YPredictor was used when Y-SNP information from studies were inadequate (e.g. no SNP's upstream of Q-M242 tested).

Samples follow a constant naming convention, with _n and _yQP_n suffixes indicating they were obtained from studies and FTDNA Projects respectively. The following populations were included;

FTDNA Y-DNA Q Migration Route
Irn = Iranian (Unspecified ethnicity), Azr_Tal = Talysh from the Republic of Azerbaijan, Trk/Tur = Anatolian Turkish, Ptn = Pashtun from Afghanistan, Ind = Indian (Unspecified ethnicity/caste), Irq = Iraqi (Unspecified ethnicity), Kzk = Kazakh, Pak = Pakistani (Unspecified ethnicity), Uzb = Uzbek, Tjk = Tajik, Haz = Hazara, Npl = Nepali, Arm = Armenian, Geo = Georgian, UAE = Emirati Arab, Irn_Arab = Iranian Arab (Khuzestan), Irn_Mzn = Iranian Mazandarani (Mazandaran), Irn_Bkt = Iranian Bakhtiari

Once collation was complete, modal haplotypes of inferred clusters were found if necessary. Additionally, clusters were inferred from haplotrees that were created. The Most Recent Common Ancestor (tMRCA) of choice clusters were calculated by comparing two modals from the first pair of intra-cluster branches. Due to the STR panels tested in the concerned papers (Y-Filer order 1) McGee's Y-Utility was the only immediately viable choice (infinite allele mutation model, 75% Probability, 25 year/generation).

Working Hypothesis
An indeterminable mix of recent (>1500ybp) and prehistoric Y-DNA Q1a-MEH2 and Q1b-M378 lines exist in the region with some instances of close haplotype sharing between West, South and Central Asia.

Limitations Of This Investigation
  • Although the number of STR panels tested has increased gradually over the past decade, 16 is not considered a "confident sell" in the genealogy world. 
  • Additionally, the difference in STR panels used meant some informative populations, such as the Makrani, Baloch, Burusho and Parsis of Pakistan were not included due to an overlap of only 12 STR's.
  • Y-STR's from several crucial populations, such as the Qashqai, Iraqi Turkoman and Azeri's from the Republic of Azerbaijan could not be found.
  • There is, of course, the great debate concerning STR mutation rates. At the time of writing I have not observed any clear consensus in the genealogy regarding this topic. The applicability of Nordtvedt's Generations series to this entry is minimal due to an STR overlap issue, hence the decision to use McGee's tool instead.
  • As discussed later, the number of Y-SNP's tested across the cited studies are insufficient to draw firm conclusions.
  • Finally, sample size is an issue. The dataset is dominated by Iranian or Afghan samples because these papers were released at times (i.e. 2008-present) where the 17 STR Y-Filer panels became mainstream. 

Y-DNA Q1a Phylogenetic Tree
Haplogroup Q1a STR Results
Four informative clusters were inferred;

  • Cluster A (DYS19=15, DYS389i=12) is largely restricted to Afghan Pashtuns, with Ptn_1-4 all sharing having a MRCA with their modal (and therefore likely founding haplotype) between 900-450 ybp. This result is consistent with the dominance of Turkic-speaking dynasties in this time period. 
  • Cluster B (DYS385a=14) has a large geographical spread from Turkey through to Iran, the United Arab Emirates, Afghanistan, Nepal and Kazakhstan. The most immediate observation is the close haplotype sharing (3-step mutation, 14/17) between Kzk_1 and Irn_4, with an estimated MRCA at 900 ybp. This result, together with the general area covered, again indicates this cluster should at the very least be broadly associated with Central Asian Turks.
  • Cluster C (DYS392=16, DYS389ii=28, DYS448=22) is interesting because its' members are exclusively Iranian and belong to Haber et al.'s Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. [2] Most of the Iranians bearing Haplogroup Q-M242 in their sample were from West Iran, where Iran's Azeri population happens to dominate the northern region. The regional exclusivity of this cluster combined with the very recent MRCA (900 ybp) lead me to suspect Haber and his associates sampled a locale in West Iran that underwent genetic drift, explaining the +10% Q-M242 that is otherwise not seen in other studies. [1] However, the MRCA too suggests these Iranian men's paternal ancestor was also associated with Medieval Turks despite the result in it's entirety not representing West Iran sufficiently.
  • Cluster D (DYS439=11, DYS437=15) mirrors Cluster B's distribution across the region but the divisions are more consistent with geography than other variables (i.e. Anatolian Turk and Armenian, Hazara together). 

Haplogroup Q1b STR Results
Five informative clusters were inferred;

Y-DNA Q1b Phylogenetic Tree
  • Cluster A (DYS385a=12, DYS439=11, DYS437=15) is, relative to the others, an early offshoot that is highly localised in South-Central Asia. 
  • Cluster B (DYS385a=14) is also localised, found specifically in Iraq and Iran.
  • Cluster C (DYS385a=14, DYS448=20) is twinned with B but appears to have a younger MRCA (925 ybp). Of interest is the wide geographic distribution across Turkey, Iran, India and Kazakhstan. Central Asian Turks once more provide a convenient historical narrative for both the predicted MRCA and spread.
  • Cluster D (DYS385a=15) is again geographically localised, this time in the greater Near-East (Turkey, Iran and Syria). 
  • Cluster E (DYS385a=12, DYS437=15) once more displays geographic localisation in South-Central Asia, specifically among Afghani Pashtuns and a FTDNA Project Pakistani.

SNP's - What Do They Tell Us?
Tabulated Y-DNA Q SNP's for select populations from several studies [1, 3-5] can be viewed in the Vaêdhya Data Sink.

There is, unfortunately, a two-pronged incompatibility issue between the Y-STR analysis and Y-SNP's provided here. Not only is there poor overlap between the populations covered in both sets, but the SNP selections in the four studies cannot do not provide us with a clear picture regarding the presence of Q*-M242(xQ1a-MEH2,xQ1b-M378) Q1a*-MEH2(xQ1a2-M25), Q1a2-M25 and Q1b-M378.

However, the distribution of Q1a3-M346 and Q1b-M378 across the Iranian plateau in contrast with the specificity of Q1a2-M25 in Azeri Iranians and Turkmen (1.6% and 42.6% respectively, although the latter is likely due to genetic drift as discussed here) suggests a strain of the first two lineages is linguistically neutral and preceded the millennia of Turkish dynastic dominance in Iran.

Fortunately, such an inference is indeed supported by the Q1a and Q1b phylogenetic trees shown in this entry. One will note (particularly with Q1b-M378) the distribution is largely geographical rather than covering large swathes of Asian land through a "recent" paternal ancestor.

A comment on Assyrian Q-M242
Although the number of STR markers tested do not allow their inclusion into this research piece, I took the liberty of comparing the sole Assyrian Y-DNA Haplogroup Q-M242 individual from the FTDNA Assyrian Heritage DNA Project to elaborate on their paternal ancestor's ultimate origins.

The Assyrian people are a Neo-Aramaic-speaking ethnic minority native to the land intersecting between Turkey, Iran and Iraq as well as the Mesopotamian basin. Modern Assyrians have (due to their Christian faith and recent historical events) practiced endogamous relationships, making them a genetically distinct group minimally affected by demic movements in the surrounding populations.

The Assyrian Y-DNA Q belongs to the Q1b1a-L245 subclade. As we have observed already, haplogroup Q1b-M378 tends to have a distribution governed more by geography with deeper cluster branches, implying greater diversification time in a given region.

At present, based on the available 10 overlapping STR's, the Assyrian Q1b1a-L245 individual matches Tur_yQP_3 best with a one-step mutation (9/10), placing them deep within Cluster C, the only one without a region-specific distribution. This preliminary evaluation indicates this Assyrian man's paternal ancestor shares Medieval genetic links with Anatolian Turkish, Iranian, Indian and Kazakh men, making a Central Asian Turkish connection likely once more.

Due to the limitations described above, the identification of clusters is more relevant based on their geographic spread. The MRCA calculations shown are simply an extremely rough estimate at the age of a cluster.

However (and fortunately once more), it is very clear that some clusters are determined by geography rather than the sort of "genealogical boon" observed in a few (e.g. Q1a Cluster C's extensive branching despite being young relative to the others).

If one takes the MRCA calculations as a very rough approximation, whilst considering a cluster's ability to supercede regional boundaries, one can estimate that 75.4% (40/53) of the Y-DNA Haplogroup Q1a-MEH2 and 31.4% (11/35) of Y-DNA Haplogroup Q1b-M378 in West, Central and South Asia can be attributed to the Turkish migrations.

In summary, Y-DNA Haplogroup Q1a-MEH2 (likely Q1a2-M25 based on anecdotal SNP evidence) is a convincing Medieval Central Asian Turkish genetic marker based specifically on its' ability to form multi-ethnic clusters in regions with a historical Turkish connection. Q1b-M378, on the other hand, generally displays enough regionalisation and cluster depth to make such an association doubtful at best, with the sole exception being those who belong to the a genetic group highlighted in this entry (Cluster C) with DYS385a=14 and DYS448=20. 

South Central Asian Q1b-M378 appears to be autochthonous whereas any form of Q1a-MEH2 in the region has a strong association with regions intimately connected with the Medieval Turks. The Anatolian highlands and the Iranian plateau, however, appear to be a complicated mix between the two based on the lack of clear distinctions.

The slim presence of Haplogroup Q in India on the other hand, as far as the current data indicates, is almost entirely of Medieval Turkic input, although the Subcontinent's position as a geographic nexus (much like Iran and Turkey) certainly open the possibility for exotic para-haplogroups to also exist there.

  • Gratitude is extended to the FTDNA Projects for making their data publicly available. Independent research ventures such as my own would not be possible without their generosity.
  • I would also like to thank Mr. Paul Givargidze, administrator of the Assyrian Heritage, Aramaic and Y-DNA J1* DNA Projects at FTDNA for providing his esteemed support on this research entry.
  • The Y-DNA Haplogroup Q migration route maps are courtesy of the Genographic Project and FTDNA.

Addendum I [5/08/2012]: It has been brought to my attention that Tur_yQP_3, the Assyrian Q1b1a's best match, is in fact an Armenian individual. Although this does not compromise the conclusions reached above, it does serve as a reminder that not everyone in the Republic of Turkey is an ethnic Turk!
Addenum II [6/08/2012]: A recent exchange on a forum highlighted the likelihood of several Turk_yQP samples being Armenian rather than Anatolian Turkish. As above, the findings shouldn't impede too greatly on what has been discussed in this entry.

1. Grugni V, Battaglia V, Hooshiar Kashani B, Parolo S, Al-Zahery N, et al. (2012) Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians. PLoS ONE 7(7): e41252. doi:10.1371/journal.pone.

2. Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA, Youhanna SC, Saade S, Soria-Hernanz DF, Royyuru A, Wells RS, Tyler-Smith C, Zalloua PA; Genographic Consortium. Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. Eur J Hum Genet. 2011 Mar;19(3):334-40. Epub 2010 Dec 1.

3. Al-Zahery N, Semino O, Benuzzi G, Magri C, Passarino G, Torroni A, Santachiara-Benerecetti AS. Y-chromosome and mtDNA polymorphisms in Iraq, a crossroad of the early human dispersal and of post-Neolithic migrations. Mol Phylogenet Evol. 2003 Sep;28(3):458-72.

4. Abu-Amero KK, Hellani A, González AM, Larruga JM, Cabrera VM, Underhill PA. Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions. BMC Genet. 2009 Sep 22;10:59.

5. Cinnioğlu C, King R, Kivisild T, Kalfoğlu E, Atasoy S, Cavalleri GL, Lillie AS, Roseman CC, Lin AA, Prince K, Oefner PJ, Shen P, Semino O, Cavalli-Sforza LL, Underhill PA. Excavating Y-chromosome haplotype strata in Anatolia. Hum Genet. 2004 Jan;114(2):127-48. Epub 2003 Oct 29.

6. Gokcumen Ö, Gultekin T, Alakoc YD, Tug A, Gulec E, Schurr TG. Biological ancestries, kinship connections, and projected identities in four central Anatolian settlements: insights from culturally contextualized genetic anthropology. Am Anthropol. 2011;113(1):116-31.

7. Roewer L, Willuweit S, Stoneking M, Nasidze I. A Y-STR database of Iranian and Azerbaijanian minority populations. Forensic Sci Int Genet. 2009 Dec;4(1):e53-5. Epub 2009 Jun 5.

8. Dulik MC, Osipova LP, Schurr TG. Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions. PLoS One. 2011 Mar 11;6(3):e17548.

9. Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, et al. (2012) Afghanistan's Ethnic Groups Share a Y-Chromosomal Heritage Structured by Historical Events. PLoS ONE 7(3): e34288. doi:10.1371/journal.pone.0034288

10. Tenzin Gayden, Alicia M. Cadenas, Maria Regueiro, Nanda B. Singh, Lev A. Zhivotovsky, Peter A. Underhill, Luigi L. Cavalli-Sforza, and Rene J. Herrera. The Himalayas as a Directional Barrier to Gene Flow. Am J Hum Genet. 2007 May; 80(5): 884–894.

11. Lacau H, Bukhari A, Gayden T, La Salvia J, Regueiro M, Stojkovic O, Herrera RJ. Y-STR profiling in two Afghanistan populations. Leg Med (Tokyo). 2011 Mar;13(2):103-8. Epub 2011 Jan 14.