In each of today's theme answers, highlighted squares contain two of the same creatures, embedded in common phrases. For example, we find two ANTs in M[ANT]OM[ANT]ALK and two CATs in [CAT]CHAS[CAT]CHCAN. Why do we have two of each? Because these five pairs are destined for the ARK (Holder of the contents of the shaded squares). Oddly, plenty of other animals appear in this puzzle, but as singles. We have a COW, a CAMEL, a NEWT, a SHREW, and a KOALA. Admittedly, the SHEEP, BISON, and ROE may be sets of two or more - we'll never know! NITS and YETIS are definite plurals, unfortunately on the one hand, and Really? on the other. A couple of other animals are mentioned in the clues (a kitten and a hedgehog - why can't he just share the hedge?). And, last but not least, I thought it was funny that the word TUB appears in the mirror-image spot from ARK.
In a vaguely coincidental turn of events, the most recent recent New Yorker includes an article about the epic Gilgamesh (wait for it), in which there's a story about a man told by the gods to build a giant vessel in which to save himself and a bunch of animals from a giant flood. My takeaway: arks are really hot right now.
In addition to the above-mentioned menagerie, there are some solid clue/answer pairs like "The limit, when there is no limit" / SKY, "Caper" / ANTIC, and "The Spouter in 'Moby Dick,, for one" / INN along with a number of other grid entries worth saving including GUARANTEE, SPACERACE, and DEADTIRED.
I didn't love RAKE for "Collect, with 'in'" but maybe that's a theme entry, too. How else was Noah going to get these animals onto the ark?