I'm not sure about that one, and I can't find any explicit text in the rules.
I know that regular HD for improved monsters also improves one ability by one point every four Hit-dices, but is it also true for "bonus HD" that the animal companion gets?
I found this in the SRD. it mentions everything besides ability scores. Do you know where I can find an explicit text in the rules?
Extra eight-sided (d8) Hit Dice, each of which gains a Constitution modifier, as normal. Remember that extra Hit Dice improve the animal companion’s base attack and base save bonuses. An animal companion’s base attack bonus is the same as that of a druid of a level equal to the animal’s HD. An animal companion has good Fortitude and Reflex saves (treat it as a character whose level equals the animal’s HD). An animal companion gains additional skill points and feats for bonus HD as normal for advancing a monster’s Hit Dice.
What speaks against just assuming it is this text from the FAQ:
The animal companion rules — or, for that matter, pretty much any other effect that grants a creature bonus Hit Dice — don’t use the monster improvement rules presented in Chapter 4 of the MM. The rules in MM are for creating tougher versions of existing monsters, not for increasing the statistics of creatures who gain Hit Dice.
An animal’s normal advancement line has absolutely nothing to do with the benefits it gains from being an animal companion, and vice versa. A wolf animal companion doesn’t become size Large when its Hit Dice increases to 4, nor is it limited to the “normal” Hit Dice cap for wolves.