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If you take the Indo-European languages out of the list you'll see that very few languages outside the Indo-European family make a masculine/feminine(/neuter) distinction.
Yes, but they are there...
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They're not completely unrelated phenomena. The Indo-European masculine/feminine/neuter distinction started out as an animate/inanimate distinction, which is what it still is in Hittite. It was only after Anatolian broke off from the rest of Indo-European that masculine and feminine began to be distinguished from each other.
We don't know. It might be a Hittite feature, influenced by some other (non-IE) language. Having an animate/inanimate distinction in Hittite doesn't mean it did exist in all other old IE languages. As far as I know, Sanskrit is very old too and it has 3 genders.