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'Animal ancestor' is just an extremely bad idea that needlessly complicates a simple concept.
Like IndigoErth said 'We used animal DNA to mutate them' would have not been hard, and it would have not have to indirectly imply that Bebop's and Rocksteady's ancestors screwed with Warthogs and Rhinos, respectively.
Alternately, if they wanted to go 'different,' they even could have mutated a rhino and a warthog, and it would have been just as easily plausible! They could have had the Turtles investigating a Zoo break-in if they wanted to add yet more OT references!
The only way I could see the Animal Ancestors thing being salvaged is if aliens turned a bunch of animals almost completely human, and a bunch of humans almost completely into animals as a way to manipulate their gene pools. Some 'stray' DNA being unaffected by this change remaining, or that with the right retro-mutagen that can undo the mutagen's bond, some 'humans' can 'return' back to what they used to be, but do to genetically intermixing with regular humans, can only turn back partway. But this would require effort in storytelling, which this movie seems severely opposed to doing.
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