Separating the post-Glacial coancestry of Europeanand Asian Y chromosomes within haplogroup R1a

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.