Unfortunately, this paper has already become outdated since being submitted for peer review at the AJPA, largely thanks to work by R1a hobbyists (see here). For instance, the authors claim that the overlap zone between R-Z280 and R-Z93 is Inner and Central Asia. In fact, these two subclades overlap in Europe, which is where most of the ancestral R-Z93 lineages have been located to date. Hopefully a major paper on R1a is on the way that will clear this up at academic level, because it's a strong hint that R-Z93 might have expanded deep into Asia from Europe.
Since the discovery of R1a1-M458, this is the first scientific attempt to divide haplogroup R1a1-M198 into multiple SNP-based sub-haplogroups. We have genotyped 217 R1a1-M198 samples from seven different population groups at M458, as well as the Z280 and Z93 SNPs recently identified from the “1000 Genomes Project”.
The two additional binary markers present an effective tool because now more than 98% of the samples analyzed assign to one of the three sub-haplogroups. R1a1-M458 and R1a1-Z280 were typical for the Hungarian population groups, whereas R1a1-Z93 was typical for Malaysian Indians and the Hungarian Roma. Inner and Central Asia is an overlap zone for the R1a1-Z280 and R1a1-Z93 lineages. This pattern implies that an early differentiation zone of R1a1-M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Eastern Europe. The detection of the Z93 paternal genetic imprint in the Hungarian Roma gene pool is consistent with South Asian ancestry and amends the view that H1a-M82 is their only discernible paternal lineage of Indian heritage.
Previous publications have pointed out that regions of highest haplogroup frequencies do not always indicate the territory of origin (Cinnioglu et al., 2004) and high STR diversity may not be exclusively an indicator of in-situ diversification but could also be the consequence of repeated gene flow from different sources (Zerjal et al., 2002; Sharma et al., 2009).
Pamjav, H., Fehér, T., Németh, E. and Pádár, Z. (2012), Brief communication: New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1. Am. J. Phys. Anthropol.. doi: 10.1002/ajpa.22167