December 04, 2012

Armenian Y-STR haplotype data

The same data was studied by Herrera et al. (2011) where it was shown that haplogroup R2 was one of the distinguishing features of the Sasun community.

I decided to try the batch version of the Haplogroup Predictor on this data, and I include my results in this spreadsheet. This is useful as test data because real haplogroup assignments and Y-STR data are known for the same individuals, so they can be cross-checked against the predicted haplogroup.

Haplogroup prediction was made on the basis of the highest posterior probability and with equal priors. There were a few errors, some of which are understandable (for example, the 23-marker version does not include haplogroup R2, so the R2 samples were assigned to various other haplogroups).

With a few other discrepancies aside (e.g., some R1b1a2 assigned to L), the overall performance seems robust, and one can probably use this tool for published Y-STR data, with the caveat that some predictions for the less frequent haplogroups -for which there were probably fewer training samples- may be off the mark.

Legal Medicine doi:10.1016/j.legalmed.2012.10.003

Sub-population structure evident in forensic Y-STR profiles from Armenian geographical groups 

Robert K. Lowery et al


Over the course of its long history, Armenia has acted as both a source of numerous indigenous cultures and as a recipient of foreign invasions. As a result of this complex history among populations, the gene pool of the Armenian population may contain traces of historically well-documented ancient migrations. Furthermore, the regions within the historical boundaries of Armenia possess unique demographic histories, having hosted both autochthonous and specific exogenous genetic influences. In the present study, we analyze the Armenian population sub-structure utilizing 17 Y-chromosome short tandem repeat (Y-STR) loci of 412 Armenians from four geographically and anthropologically well-defined groups (Ararat Valley, Gardman, Lake Van and Sasun). To place the genetic composition of Armenia in a regional and historic context, we have compared the Y-STR profiles from these four Armenian collections to 18 current-day Eurasian populations and two ancient DNA collections. Our results illustrate regional trends in Armenian paternal lineages and locale-specific patterns of affinities with neighboring regions. Additionally, we observe a phylogenetic relationship between the Northern Caucasus and the group from Sasun, which offers an explanation for the genetic divergence of this group from other three Armenian collections. These findings highlight the importance of analyzing both general populations as well as geographically defined sub-populations when utilizing Y-STRs for forensic analyses and population genetics studies.


Link

5 comments:

aspromavro said...

The link to the spreadsheet is not working.

andrew said...

The implication of R2 in this community would seem to be a population genetic link to South Asia (particularly Pakistan) and Eastern Iran. Sasun ethnogenesis seems to date to roughly the same period of likely South Asian migrations involving the Roma and the people of Cres Island (i.e. the tale end of the migration period). Alternately, one could imagine the Sasun as a remnant population of the Indo-Aryan Mittani incursion.

South Central Haplo said...

Being recipient of foreign invasions and right in the middle turkic tribal expansion. few C,Q,N( 1 each). Very few R1a. Mostly West Asian with South Asian mix.

Onur said...

Being recipient of foreign invasions and right in the middle turkic tribal expansion. few C,Q,N( 1 each). Very few R1a. Mostly West Asian with South Asian mix.

In some Y-chromosome studies Armenians show much higher proportion of R1a (e.g., close to 10%) than in this study. I suspect that there is significant regional variation in the proportion of R1a among Armenians. BTW, 10% R1a is normal for West Asia, especially for its northern parts such as Asia Minor, the Armenian Highland, the Caucasus, Syria, northern Mesopotamia and much of Iran.

superscript98 said...

Sasun ethnogenesis seems to date to roughly the same period of likely South Asian migrations involving the Roma

The problem with this claim is that R2a is actually rare among the Roma. I find it hard to believe that the Armenian R2a is Roma related considering that the actual diversity of this lineage among the Armenians and in the Middle East in general is quite high. If it was Roma related, it would show very little diversity.

The other thing we need to keep in mind is what kind of R2a are they carrying? The latest major subclade of R2a is R2a1 (L295). Here's the distribution map of R2a based on the R2 FTDNA project (Blue is R2a1-L295+ while red is R2a-M124 that tested negative to the L295 SNP):

http://img835.imageshack.us/img835/4351/39102208.jpg