Showcasing of Y-DNA Variation Among Afghan Ethnic Groups [Review]

This very recent paper on Afghan Y-Chromosomes was released by M Haber et al. and provides us with an insight into the paternally-determined genetic structure of several Afghan populations.

Afghanistan's Ethnic Groups Share a Y-Chromosomal Heritage Structured by Historical Events
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

"Afghanistan has held a strategic position throughout history. It has been inhabited since the Paleolithic and later became a crossroad for expanding civilizations and empires. Afghanistan's location, history, and diverse ethnic groups present a unique opportunity to explore how nations and ethnic groups emerged, and how major cultural evolutions and technological developments in human history have influenced modern population structures. In this study we have analyzed, for the first time, the four major ethnic groups in present-day Afghanistan: Hazara, Pashtun, Tajik, and Uzbek, using 52 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y-chromosome. A total of 204 Afghan samples were investigated along with more than 8,500 samples from surrounding populations important to Afghanistan's history through migrations and conquests, including Iranians, Greeks, Indians, Middle Easterners, East Europeans, and East Asians. Our results suggest that all current Afghans largely share a heritage derived from a common unstructured ancestral population that could have emerged during the Neolithic revolution and the formation of the first farming communities. Our results also indicate that inter-Afghan differentiation started during the Bronze Age, probably driven by the formation of the first civilizations in the region. Later migrations and invasions into the region have been assimilated differentially among the ethnic groups, increasing inter-population genetic differences, and giving the Afghans a unique genetic diversity in Central Asia."

[PDF] [Supplementary Data]

Tabulated Y-DNA Haplogroup frequencies of the 204 individuals sampled distinguished by ethno-linguistic affiliation (ISOGG 2011 Nomenclature utilised) can be found in the Data Sink.



Results (populations sample count ~50 only)

- Haplogroup B-M60, a marker that would normally be expected among African populations, makes a surprising presence in the Afghan Hazara. Superficial STR analysis (17/19 haplotype match between all) suggests a recent common paternal ancestor, although the timeframe and ultimate origin of this common ancestor is another question.

- Haplogroup C3-M217 has invariably been associated with the expansion of Altaic-/Mongolic steppe populations since medieval times. The greater frequency (33.9%) in the Hazara relative to the Tajiks and Pashtuns appears to support this, as well as the commonly-held belief they partially descend from Mongolian tribes.

- The Hazara E1b1b1c1-M34 also stems from a common ancestor (all three share the exact 19 STR haplotype).

- The single man belonging to Haplogroup G1-M285 is of Tajik descent. It is possible this man's paternal line arrived with eastward migrating Persians following the Sassanid collapse in 651 A.D.

- As shown in previous studies, the Pashtun Haplogroup G men are again G2c-M377 (entirely this time, in contrast with Lacau et al.)

- Paragroups H*-M69, J2a*-M410, Q*-M242 and R*-M207 all indicate that Afghanistan played an important role in the demic development of their downstream subclades, or was at the very least a geographic nexus. It is worth noting that the Hazara Q* men belong to a different haplotype to their Pashtun and Tajik compatriots, again indicating genetic drift has taken place since the formation of the Hazara ethnic group (or, instead, paternal consistency through the presumed Mongolic layer that eventually formed modern Hazaras).

- In previous studies (Sengupta et al., Lacau et al.), several haplotypes without backbone SNP testing were found to belong to Haplogroup I, which is frequently considered a lineage specific to Europe. For the first time we have evidence of an I clade (I2b1-M223) in South-Central Asia, specifically among the Hazara and Tajik. The following is a recent exchange with Professor Ken Nordtvedt regarding the I2b1-M223 samples;

"The two Hazara seem related.  Both haplotypes look like M223+, with the Tajik one like Continental2 characteristic of central Europe.
The Hazara haplotype looks more like M223+ Roots.  But both have some problems with being considered close matches to European haplotypes.
...
I don’t think such tmrcas would be worth much.  I still don’t have a firm subclade of M223 to work with for either haplotype."

Due to the limited STR's it is not possible to cleanly place these I2b1 haplotypes into any of the existing clusters/subclades. However, Haplogroup I2b itself appears to be thousands of years old (Nordtvedt's I tree, final page). This opens up the possibility for an endogenous form of Haplogroup I existing in South-Central Asia.

- A single Tajik belonging to J1c3-P58 was postulated to potentially be of Arabian origin. As the (miniscule) Afghani Arabs did not yield any J1c3, other possibilities should be considered, such as contacts with the Iranian plateau over the past few millenia.

- The Tajiks were the only population to boast the presence of all major subclades within Haplogroup L (L1a-M27, L1b-M317, L1c-M357). In line with their greater frequency relative to the Tajiks and Hazaras, several Pashtun L1c-M357 samples share similar (exact-to-2-step mutation) matches, suggesting another example of genetic drift.

- Although the Laghman Pashtuns share a similar L1c-M357 haplotype (16-17/19 match), so does the sole Tajik L1c from the same location, providing us with genetic evidence of recent mutual origins between Pashtuns and Tajiks in certain parts of Afghanistan.

- The Tajik population is more paternally diverse than all others sampled. Explanations include a less endogamous cultural character or the more recent imposition of the "Tajik" identity, which arrived with the medieval Turks.

- R1b1a*-P297 (xM269) and R1b1a2*-M269 (xU106) both appear in Uzbek and Tajik populations. Both the R1b1a*-P297 haplotypes are identical and belong to a Tajik and Uzbek, again showing there is some recent paternal overlap between Central Asian ethnic groups. I discovered the haplotype does not generally correspond with any of the established clusters in the R1b1a1-M73 Project, although there is a 13/15 match with a Tajik from Cluster B1. Although the limited STR's are unfavourable, I am of the opinion the match is substantial and the R1b1a*-P297 reported in this study is in fact R1b1a1-M73 and belongs to Cluster B1, whose membership also consists of other Tajiks, Uzbeks and an Anatolian Turk.

- It is very interesting to note that all the locations showing R1b1a*-P297 (xM269) and R1b1a2*-M269 (xU106) (Badakhshan, Herat, Takhar and Mazar-e-Sharif) lie on a horizonal plane that runs across the north of Afghanistan, particularly as the Bactria-Margiana Archaeological Complex (BMAC) was situated here.


Criticisms of Paper

- Haplogroup R2a-M124 has been erroneously correlated with aboriginal Subcontinental populations when results from the R2 WTY Project indicate places like India are a "sink" rather than a "source" (most Indian R2a is R2a1-L295, which has a spotty distribution across the rest of Eurasia).

- Haplogroup L is, much like R2a, an understudied lineage, presumably due to its' paucity in Europe. The once-common assumption in the population genetics and genealogical world that the frequency of a given lineage in a region/population signifies its' antiquity there has been proven to be inherently false through STR and SNP analysis. Haplogroup L may enjoy greater frequencies in India according to the sources at their disposal, but the presence of different L subclades in Central and West Asia should have at least given the authors the initiative to investigate the lineage's deeper structure rather than relying on a population genetics tagline from at least 2006 (Sengupta et al.).

- Despite the recent boon in research on Haplogroup R1a1a-M17's structure by independent genetic genealogists and projects (such as the R1a1a and Subclades Y-DNA Project), Haber et al. failed to include any of the pivotal SNP's that have been discovered since Underhill et al. from 2009, thus preventing observers from making any meaningful conclusions from the current findings, particularly in the context of the Indo-European migrations (generally accepted from the Eurasian steppes).

- When divided into ethno-linguistic lines, this study showcases 3 Arabs, 13 Balochis, 59 Hazaras, 5 Nurestanis, 49 Pashtuns, 56 Tajiks, 1 Turkmen and 17 Uzbeks. The most immediate criticism is inadequate testing of the Arabs, Nurestanis, Balochis, Turkmens and Uzbeks in particular.


Evaluation

Despite several glaring flaws in methodology, Haber et al. has provided us with a much-needed insight into the deeper genetic structure of Afghanistan's Y-Chromosome diversity. There is clear evidence of genetic drift (particularly among the Pashtun Q*-M242/L1c-M357 or Hazara C3-M277), as well as evidence of recent line sharing between populations (The situation of L1c-M357 in Laghman).

However, Haber et al. has thrown out some very interesting surprises (T1-M70 among Tajiks only) as well as validating results from previous studies that had previously been questioned (I2b1-M223 and R1b1a2-M269 particularly). How did these lineages arrive in Central Asia? Is recent colonial admixture a possibility? For the time being, we will have to contend with this questions steadfastly.


Addenum I [30/03/2012]: Determination of R1b1a*-P297 furthered with regard to it potentially being R1b1a1-M73.
Addenum II [30/03/2012]: Insertion of Nordtvedt correspondence.

Of Buryats and Kalmyks: The R2a connection [Original Work]

Introduction
The following is an investigation I conducted of the Y-DNA R2a-M124 Siberians found in Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a;

"To investigate the structure of Y chromosome haplogroups R-M207 and Q-M242 in human populations of North Asia, we have performed high-resolution genotyping using both single nucleotide polymorphisms and short tandem repeat (STR)-based approaches of 121 M207- and M242-derived samples from 885 males of 16 ethnic groups of Siberia and East Asia. As a result, the following Y chromosome haplogroups were revealed: R1b1b1-M73 (2.0%), R1b1b2-M269 (0.7%), R2-M124 (1.1%)..."

Supplementary information can be found here.

The 10 R2a-M124 individuals were either Buryat (4/10) or Kalmyk (6/10), two Mongolic-speaking populations living in the Republic of Buryatia (South Siberia) and Republic of Kalmykia (northwest Caspian coast) respectively. It is worth noting, however, the Kalmyk sample was probably not from Kalmykia given the authors specified their participants were "...from 885 males of 16 ethnic groups of Siberia and East Asia". Thus, the results of the investigation (and the R2a-specific analysis here) may not be applicable to the Kalmyk majority of Kalmykia.

R2a haplotypes

All the R2a Siberians belonged to the same 12 STR haplotype apart from two Buryats, whose haplotype differed from the others only by a 1-step mutation at DYS389II (16 -> 17). Adjacent is a spreadsheet comparing the Buryat and Kalmyk haplotypes with raw data from the R2 FTDNA Project, which contains 62 participants who have tested to 67 markers. A legend can be found on the bottom of the attached comparison. Please also note that DYS389II in this instance is the sum between DYS389I+II found on the spreadsheet, as per the standard used by SMGF and FTDNA (DYS389II should've really been called DYS389B!).

Results

• The paucity of 12/12 matches (or even 1/2-step) alone indicate these Siberian R2a's are divergent to the R2 project participants beyond the genealogical time frame. Therefore, we can already surmise none of the Jewish, Iranian, Indian, European or Near-Eastern R2a's in the project are recently related to them.
• Deeper analysis of the Buryat and Kalmyk haplotypes through McGee's Y-Utility reveals the MCRA (Most Common Recent Ancestor) was roughly 900 years ago based on the single one-step mutation on DYS389ii (Infinite allele mutation model, 30 years/gen, constant mutation rate of 0.0024). This date (~1100 A.D.) coincides with the rise of Mongolian steppe dominance and falls just short of Genghis Khan's reign. Based on the above, it is likely the haplotype differentiation happened in historical times and the common ancestor was a native of the region.
• Comparing the Buryat and Kalmyk haplotypes with the R2 project participants with the Y-Utility again demonstrates their great divergence. The earliest match to both is a Syrian paternal ancestor (1530-2190 y.b.p.). All other matches are invariably between 2970-7530 y.b.p. with little geographical coherency. This is likely an artefact of the limited number of STR's.

Summary
Although the number of STR's has limited the scope of this investigation, the Buryat and Kalmyk R2a haplotypes display a striking degree of exclusivity from other Eurasian R2a's and match each other well enough to conclude a recent mutual ancestor pre-dates the two and was likely a native of the region, probably around Genghis Khan's era. The twelve STR's alone have safely shown that R2a in Siberia is not of recent South Asian origins, indicating a greater antiquity in Siberia as well as Central Asia, which is presumably the source location.

Additional

Phylogenetic tree

Phylogenetic tree showing degree of relatedness between Buryat and Buryat-Kalmyk haplotypes relative to the R2a FTDNA Project participants on the 12 STR's used in this investigation (shown opposite). FITCH and FigTree used to generate. Special thanks to vineviz for elaborating on their application. Inferences should be made with plenty of caution given the low number of STR's, but it is interesting to see the Syrian match appear again.

Through this investigation I have inadvertently coined a "Mongolian" R2a Haplotype (i.e. mutual Buryat and Kalmyk) defined by the following STR's;

DYS393 DYS390 DYS19 DYS391 DYS385 DYS439 DYS389i DYS392 DYS437 DYS43814 23 14 10 12-19 10 12 10 16 11

In a study by Nasidze et al. on 99 Kalmyk men, the exact same haplotype shown above was observed. Although the earlier (justified) warning of this investigation's results being extrapolated onto the Kalmyk's living in Kalmykia, it was clearly without merit; the Republic of Kalmykia R2a haplotype is an exact match with the Mongolian one identified here. Therefore, at least some of the R2a found in Kalmykia is a direct import from Siberia rather than nearby sources, such as the Caucasus.

Through this independent investigation, I have demonstrated that the antiquity of R2a outside the Indian Subcontinent is very understated and haplogroups existing at background frequencies may have their own interesting stories to tell.