What decides which subrace your leader gets modified to?

[Nakkivene]

Modify entire race, sure, the central intelligence gets modified to that.

Modify one generator world, all of a sudden he loses his +2 leadercap trait. Okay?

Modify third of the population, he remains the previous modified species.

How does this work?

 

[Sigma 582]

Each leader, including rulers, is linked to certain pop in your empire. When you modify the pop, the leader's traits change accordingly.

Same is true for gestalt rulers, even though many would say it doesn't make sense.

 

[Nakkivene]

Ah, and which pop this is is up for guesswork?

 

[RabbaDooDabba]

I would guess it uses the founder-species-template found in the demographics tab

 

[jdrou]

Each leader, including rulers, is linked to certain pop in your empire. When you modify the pop, the leader's traits change accordingly.

There's no indication in the savegame of leaders being linked to specific pops, just species. I think it just changes leaders randomly based on what fraction of the species you modified.