It's the difference between using the 'il' preposition and the 'lo' preposition. You use 'lo' before a word beginning with a 'z', or an 's'+consonant (like, "squalo"). In this case, we're talking about "lo zoo", so it becomes "nello" (in+lo=nello)
in+il=nel in+lo=nello in+la=nella
Also: in + l' = nell', in + gli = negli, in + le = nelle, in + i = nei. There are similar contractions for the prepositions "a", "da", "di", and "su", when followed by the same definite articles (il, lo,la, l', i, gli, le).
There was a table with all of these contractions in the "Tips and notes" for "Basics 2", before the crown levels were added. I don't see it now. Or maybe these tips have moved, but I haven't found them yet?