R1a1a is one of the most geographically expansive Y chromosomal haplogroups. It spans the Irish Sea to the Bay of Bengal. I am of this lineage, as is my friend Daniel MacArthur. But with deeper exploration of the phylogeny of this haplogroup it seems clear now that it is very diverse, with a great deal of geographic structure. There are a wide range of South Asian lineages, but also one very dominant one in Eastern Europe.
A new paper in Nature Communications, Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites, addresses a peculiarity in the domain of Jewish genetics. The Levites, the helpers of the Cohen priestly class, seem to be carriers of R1a1a, and this lineage has exploded rapidly in this population (the classic “star-like phylogeny”). The historical genetic question though is this: are the Levites descendents of a Slav proselyte? Within Europe R1a1a exhibits the highest frequency in what was once the Pale of Settlement, so this is a reasonable question.
Using whole genome analyses and more extensive geographic coverage, the answer to this question seems to be no. Rather, the Levites descend from a distinct West Asian branch of non-European R1a1a. This is evident in panel A of Figure 1. You can see clear that the Ukrainian samples are the outgroup in relation to the other branches of R1a1a. And within those there is further structure, as the South Asian Gujaratis are distinct from the clade in which most of the Ashkenazi Levites are nested (the authors posit that the presence of the Iberians may be attributable to the Moors, plausible enough). The Golden Age of Y chromosomal phylogenies is over, but these markers still have some juice which can be squeezed out.