(Watch this space for my comments once I read the paper).
UPDATE (Nov 05):
This paper makes a very important contribution by studying the diversity and distribution of Y-chromosome marker M458 defining the new haplogroup R1a1a7.
R-M458 reaches high frequency and diversity in central and eastern Europe. It is virtually absent in northwestern Europe, the Near East, and Asia east of the Urals. The maximum frequency is reached in south (36.4%) and central (33.3%) Poland.
The earliest expansion time for R-M458 is found in Poland (10.7ky), but since the paper uses the effective mutation rate that I criticized elsewhere, this date should be divided by a factor of 3 giving an age of 3.6ky. This matches quite well the age for the Balto-Slavic split according to Gray and Atkinson. As with the recent paper on J-P58, adopting the germline rate makes excellent sense.
If R-M458 had started expanding 10.7ky ago, then by the time of the early dispersals of Kurgan groups east, it would have been present among them, and we would expect to find it east of the Urals and in the Near East/Central/South Asia. To reconcile this age with the archaeological picture of west-east movements across the steppe seems impossible. However, the situation resolves itself neatly when we realize that J-P58 is only 3-4 thousand years old, and was not in existence at the time of the Kurgan expansion.
However, the paper also is inconsistent with an origin of R-M17 either in a glacial refugium or with the expansion of the Kurgan culture, as the diversity of R1a1a*(xR1a1a7) is not particularly high in either Russia or the Ukraine and is much higher in India and Pakistan:
Analysis of associated STR diversity profiles revealed that among the R1a1a*(xM458) chromosomes the highest diversity is observed among populations of the Indus Valley yielding coalescent times above 14 KYA (thousands of years ago), whereas the R1a1a* diversity declines toward Europe where its maximum diversity and coalescent times of 11.2 KYA are observed in Poland, Slovakia and Crete.
Hopefully we will not have to wait another decade for the R1a1a* chromosomes to be further resolved, and thus yield signal(s) specific to the archaeologically attested trans-Ural spread of the Kurgan culture and/or the Indo-Iranians.
There are also other useful conclusions that we may draw from this study:
1. The presence of R1a in Scandinavia does not reflect any sort of Balto-Slavic admixture, as R-M458 is lacking in them. This, coupled with the discovery of R1a chromosomes in ancient remains from Eulau and Lichtenstein in German territory suggests that R1a was present among ancient Germanic speakers. However, there is also structure in R-M458 frequency in Germany itself, with lowest percentages reached in the north and west; this suggests an admixture with Baltic and/or Slavic elements in present-day Germany itself.
2. In several Balkan samples the frequency of R-M458 ranges between 0-12% which is at most a third of its maximum frequency, suggesting that the extent of Slavic admixture in the Balkans is upper-bounded by about 1/3. The complete absence of R-M458 in Italy and its sub-1% representation in Anatolia further support the idea that R-M458 in the Balkans is of medieval and later origins.
3. The samples from Greece (N=263), Macedonian Greeks (N=57), and Crete (N=361) have R-M458 frequency of 4.2, 8.8, and 2.2%. Assuming a frequency of R-M458 at 36.4% in ancestral Slavs, as in south Poland, the admixture estimates are 11.5, 24, 6%. These should probably be interpreted as upper limits (plus statistical margins) because the highest present-day frequency of R-M458 is probably lower than that in early Slavs.
4. Interestingly, the Slavs of FYROM have an R-M458 frequency of 3.8%, barely different from that of Greeks at large, suggesting that (i) the claims of some Greek nationalists that they Slavs of FYROM are newcomers to the Balkans are wrong, just as (ii) the claim of some FYROMian nationalists that they are markedly different from Greeks are wrong. The actual truth is that the Slavs of FYROM are largely of old Balkan (pre-Slavic) stock who adopted a non-Balkan Slavic language, just as the modern Turks are largely of old Anatolian (pre-Turkish) stock who adopted a non-Anatolian Turkic language.
European Journal of Human Genetics doi:10.1038/ejhg.2009.194
Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a
Peter A Underhill et al.
Human Y-chromosome haplogroup structure is largely circumscribed by continental boundaries. One notable exception to this general pattern is the young haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestry of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorly understood as no marker has yet been described that would distinguish European R1a chromosomes from Asian. Here we present frequency and haplotype diversity estimates for more than 2000 R1a chromosomes assessed for several newly discovered SNP markers that introduce the onset of informative R1a subdivisions by geography. Marker M434 has a low frequency and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. Conversely, marker M458 has a significant frequency in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 chromosomes present there. The diversity and frequency profiles of M458 suggest its origin during the early Holocene and a subsequent expansion likely related to a number of prehistoric cultural developments in the region. Its primary frequency and diversity distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.