haplogroup diversity in the context of genetic diversity

Question

I'm just an average Joe trying to understand the context through the simplest explanation.

When I read World Map of Dominant Y-DNA haplogroups distribution, it echoes "differences among human". But then I recall that all humans are genetically more than 99% the same.

For example I remember reading a research paper that said the genetic difference between northern kalahari bushmen (A dominant) and southern ones are much greater than between chinese (O dominant) and french (R dominant), which is not reflected in "haplogroup pie chart" of aforementioned world map.

How to put this haplogroup diversity in the context of "we are 99% the same"? Is haplogroup diversity within the < 1% difference?

EDIT:

I think the map is this one https://www.pinterest.at/pin/136585801178324969/

the bushmen article is from one of paper from https://www.ncbi.nlm.nih.gov but I forgot which

Answer 1

First, the map that you referring to in plaintiff is about haplogroup distribution and thats all. Difference in genetic (drift) mostly goes linear with time. Hence the proper way is by using a tree diagram as shown in the Wikipedia page about haplogroup, which as you mentioned seen with khoi-san on top of tree as the oldest branch. The lower the branch, the less difference it makes.

Yes, genetic difference in DNA study has been controversial as it is often abused to strengthen old racism instead of eradicating it. e.g. Neanderthal remnant debacle that almost made Europeans feel exclusive until it was found out otherwise. The naming of RxR1, ExE3b or the often separately labeled R1a and R1b. You could feel immediately the new age racism via DNA, all of these despite differences being less than 1%.