"New" R1a1 SNPs

New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1:

Despite the limited data available for Z280 and Z93, some general inferences can be drawn from the geographic distributions of these two haplogroups. The R1a1- Z280 subclade is a strong candidate for covering the R1a1a* (xM458) in Eastern Europe, which was found in high frequency by Underhill et al. (2010).The tested set of 53 Malaysian Indian samples presented 100% frequency for the R1a1-Z93 subclade, without co-existence Z280 or M458 sub-haplogroups. Inner and Central Asia seem to be the overlap zones for the R1a1-Z280 and R1a1-Z93 chromosomes as both forms were observed at low frequencies. This is again consistent with the observations described for R1a1a* spread in Central Asia and in the Altai region by Underhill et al. (2010). This pattern suggests that the origin of R1a1-M198 arguably occurred somewhere between South Asia and Eastern Europe. Potential candidates could be the Eurasian Steppes (Ukraine – Southern Russia – Kazakhstan – Caucasus) or the Middle East. European populations showed higher M458 and Z280, whereas Asian populations presented higher Z93 frequencies, indicating that the new markers can be effectively used to distinguish between the European and Asian branches of the haplogroup R1a1-M198. [. . .]

The coalescent time calculated by us for R1a1-M458 carriers is consistent with the age calculated by Underhill et al. (2010) in Europe yielding 7.3 KYA versus 7.9 KYA (thousands of years ago). Underhill et al. (2010) also noted the potential association of R1a1-M458 with the Linear Pottery Neolithic culture in the territory of present-day Hungary—this observation is supported by our data. The TMRCA calculated for R1a1-Z280 diversification (10.3 KYA) is approximately in agreement with the estimation of Underhill et al. (2010) for R1a1a*(xM458) chromosomes in Eastern Europe ( 11 KYA). However, the coalescent age of 10.3 KYA for R1a1- Z93 chromosomes in this study is lower than that of populations of the Indus Valley (14 KYA) for the STR associated diversity of R1a1a*(xM458) chromosomes calculated by Underhill et al. (2010).

Of course, these markers and other markers defining additional layers of structure under M417 have been known for over a year. Budgetary constraints and the magic of peer review combine to render this paper relatively uninformative. One of the authors explains:
I have to agree with all, but those who never tried to push an article through a serious academic journal has no idea how difficult this is. The first version was submitted like 1 year ago, and also contained pedigree rates plus 500+ FTDNA samples from different ethnic groups. But unfortunately the reviewers were so narrow-minded that we had finally to drop all FTDNA samples plus the pedigree calcs.

Personally I also do not consider Zhiv. rate valid, but I had to accept this compromise to get the paper accepted. Anyway, as Lukasz pointed out, the main goal was to introduce Z93 and Z280 into the "academic circles" so in the future we may have a comprehensive paper from a more wealthy lab. The Budapest forensics are not full of money so we had no chance to have more than 12 markers tested and "low-chance SNPs" like Z284 in Hungary. Actually we submitted the first draft before Z283 was established securely on the FTDNA tree so we could not include it later...

My comments from last year on the dna-forums postings of an Underhill(lab that brought us Zhivotovsky "evolutionary" mutation rates)-affiliated academic stand:
Another poster points out: "Dividing by 3 [to bring the estimate more in line with real mutation rates] gives an age of 3300 years, almost exactly the estimate from Nordtvedt's spreadsheet." Someone else recently estimated the TMRCA for L342.2+ at around 3,600 years. So: if current patterns hold, the bulk of South Asian R1a unambiguously falls within European R1a variation. While I fully expect, when we eventually see results for these markers in large academic samples published, the papers will feature evolutionary mutation rates and less than parsimonious attempts to fit the distribution of M417 sublineages to archaeology, it's pretty clear to me Z93 and L342.2 originated on the Steppe within the past 4000 years or so and spread with Indo-Iranian.
Again: the most straightforward interpretation of the evidence is that Z93 is a relatively young branch of an evidently European lineage. Accurate, unbiased dates using SNPs instead of STRs should be here soon enough, definitively settling this and other issues.


Randolph said...

I've kept up with this for some time. Apparently Indian academics really don't want the r1a-is-from-outside-of-India argument to be true because it would have implications, i.e. that the Aryan migrations* did not actually happen/the developments were autochthonous. This line of reasoning has never made sense to me because if that's true it implies an Indian origin for Indo-European peoples in general, which seems like a big stretch - for example, if it were true, then why don't other haplogroups diagnostic of the Indian subcontinent appear in Indo-European speaking peoples elsewhere (being that these are distributed throughout the Indian populace)? It seems this question is never even considered among the proponents of the out-of-India hypothesis. I'd say it's an example of ideology taking precedence over objectivity. Any thoughts on this, n/a?

*My own understanding is that this was probably just one of many events of gene flow into India from western Eurasia, which go as far back as the lithic ages. This position evidently even has some support among Indian academics.

n/a said...

I agree attempts to prove "out of India" for R1a generally seemed ideologically motivated. I'm not sure to what to attribute the supposed high STR diversity of South Asian R1a previously reported by some Indian academics. Perhaps laboratory error or active data massaging played some role. Regardless, the SNP phylogeny makes clear Indian R1a is relatively non-diverse and removes any doubt that it arrived in South Asia via Europe and/or Central Asia.

RC said...

You base your conclusions on a weak paper. Kivisild et al showed quite conclusively that M458, found at 70% plus in many European countries and almost never lower than 30%, is completely absent outside Europe, thus making gene flow to India highly unlikely, even from Eastern Europe (the other epicenter of R1a1 diversity).

For more explanation, take a look at http://forwhattheywereweare.blogspot.ca/2012/10/finally-some-inmproved-knowledge-of.html

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