Roughly speaking, the official line of the Kyrgyz Republic is that there was a mass migration of Yenisei Kyrgyz to modern day Kyrgyzstan some time after the Yenisei Kyrgyz overran the Uighur Khaganate. Common Y-DNA descent (r1a-z93) is presented as proof of not only supposed cultural link but also genetic one between modern Kyrgyz and Altai/Khakas populations. However Kyrgyz are predominantly R1a1a1b2a, and Altai people are R1a1a1b2.

"In the complementary R1a-Z93 haplogroup, the paragroup R1a-Z93* is most common (>30%) in the South Siberian Altai region of Russia, but it also occurs in Kyrgyzstan (6%) and in all Iranian populations (1–8%). R1a-Z2125 occurs at highest frequencies in Kyrgyzstan and in Afghan Pashtuns (>40%)."


Peter A Underhill European Journal of Human Genetics 23, 124–131 (2015)

I did not find any information on the approximate date of subclade separation. Any thoughts?

It seems that in all cases clinical distribution emerges out of the mountains (Altai, Kyrgyzstan, Tajikistan, Afghanistan) and that high frequency of Kyrgyz r1a (more than 60% according to some studies) comes from remnants of Indo-european Scythians whose Y-DNA survived in mountainous areas during proto-Turkic and Mongol expansions. Kyrgyz are apparently linked to Pashtuns and Tajiks who also live in the mountains to the south and not to Siberian founder effect subgroup. But the main question is when did the two subgroups separate?