The study supports the idea of multiple waves of R1a into the Indian subcontinent, with atleast two prominent ones seperated by a time interval. 3/3 #R1a

Our analysis of R1a haplotypes showed lineage sharing between southern Brahmins and the western Iranians. Northern Brahmins experienced a rather recent mixture with R1a haplotypes similar to those found in Afghanistan. 2/3

Yes, I think a lot depends on the "weighting" given to parts/patterns of the data. What could be done with an ARG may not be possible with PCA. I have noticed a change in the clustering pattern for Indian populations (with differing demographic histories) before and after LD pruning.

Thank you for sharing this paper. @sashagusevposts.bsky.social then the LD regions should greatly influence the number of variant differences. Two African groups with different demographic history may exhibit different set of LD regions resulting in dissimilarity compared to an European group.?

How important is it to account for LD in a PCA given that some populations are bottlenecked and some are not? Uniform LD pruning would erase the very characteristic of a population (similarity/dissimilarity) which is the basis of PCA. Isn't it?