As many of you know around the year 2000 the analyses of Y chromosomal human lineages became a pretty big deal. The reason these lineages are important and useful is that they record the uninterrupted ancestry of males, from father to son, along the Y chromosome. Instead of the complexities of the whole genome, as with mtDNA you have a simple and elegant phylogenetic tree to interpret. The clusters along this tree are defined as broad haplogroups, united by derived states from a common ancestor. One of the largest haplogroups is R1a1a. It happens to be my paternal lineage, as well as Dr. Daniel MacArthur’s and Dr. Zack Ajmal’s.
The map above illustrates the peculiarity of R1a1a: it is geographically enormously expansive. How to explain this distribution? A naive response might be that this distribution is surprising similar to that of the Indo-European languages. Unfortunately this runs up against the conundrum that low caste South Indian groups, relatively untouched by Indo-Aryan culture (at least until the past few hundred years), also manifest high frequencies of R1a1a.
To make a long story short it seems that R1a1a is an old haplogroup with a lot of structure across Eurasia. Maju points me to a paper in American Journal of Physical Anthropology which simply & elegantly brings home to us some obvious insights, New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1: