It's a relatively new territory (mid 17th century) as most of Siberia. Native Russian lands are located in 'Central Russia' (geographically those are actually the most western territories of Russia, some regions of Belarus and Ukraine).

The reason for low ethnic Russian population is very simpe - it's too cold there and locals were very hostile towards Russians, there was almost no reason for making settlements there. When cossacks advanced through Siberia they tended to stick to southern border, which resulted in cities like Irkutsk.

Harsh climate was also a reason why those territories were difficult to subjugate.

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Other pink areas are north Caucasus (south-western region, 18-19th centuries) with very hostile natives and Tuva (begining of 20th century, the newest territory of Russia).