A few Hanna Barbera/Filmation cartoons are involved in a grim timeline.
While in Europe, Dr. Quest (Johnny Quest) discovers medieval text that details two species of small creatures with human-like intelligence and culture, one forest-dwelling and another aquatic. These were known to be Smurfs and Snorks. Dr. Quest attempts to create "intelligent" animals by splicing Smurf/Snork DNA with that of regular animals. Numerous test subjects such as Scooby Doo, Magilla Gorilla, Top Cat, Yogi Bear, etc. escape and contaminate local wildlife.
The animals become more intelligent and start to help humans out. Some gain a reputaton for being superheroes, like Atom Ant, Secret Squirrell, Hong Kong Phooey, and others.
The government attempts to create their own robotic replacements for these superhero animals, like DynoMutt, Frankenstein Jr, and others. After this plan fails, the government turns to South America to re-animate extinct animals, such as dinosaurs. (Dino Boy, Valley of the Lost Dinosaurs, etc.)
As intelligent animals begin to populate Earth and become a true threat to humans, the scientific/artistic/political elite go into hiding, leaving the Earth's surface, retreating to the skies, colonizing the ocean floor. (The Jetsons, Sealab 2020, The Herculoids, Space Ghost, etc.)
Due to constant war, violence, and a lack of civility, both humans and animals regress into a prehistoric, simplistic state. (The Flintstones, Mightor, He-Man)
After thousands upon thousands of years, the intelligent animals "evolve" back to their former glory and rebuild Earth, creating their own civilizations and cities. (SWAT Kats, Street Sharks, Fish Police)