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"Dogs are the leaders of the planet. If you see two life forms, one of them's making a poop, the other one's carrying it for him, who would you assume is in charge?"
—Jerry Seinfeld, Seinfeld
So let's say that the aliens land tomorrow. It's not an Alien Invasion (not even a well-meaning one); this group of aliens geniunely comes in peace. After recovering from the initial shock of realizing that, yes, other lifeforms do exist out there, the governments of the world decide to allow them to land -- which they decide to do in your back yard.
Everyone important shows up -- the President, the news crews, foreign ambassadors, UFOlogists, the mayor, and the local high school marching band. You're there, of course -- it's your yard, after all, and no one's going to evict you just because some aliens are coming to town. Your pet rottweiler is there, too, chained up beside its doghouse and its water dish.
As the aliens' Flying Saucer lands, the crowd "ooh"s and "ah"s just like crowds do. The hatch opens, and the aliens step out, repeating their message of goodwill -- to your rottweiler.
What happened here? The aliens Mistook the Dominant Lifeform of Earth, that's what.
This is a common subversion of the typical First Contact scenario. The aliens, in their studies of Earth, conclude that someone other than humanity are the real masters of Earth. Maybe they assume that we're the servants of our pets rather than mere caretakers. Maybe they're mechanical beings who aren't used to dealing with carbon-based life and assume that any intelligent beings will be machines like themselves. Maybe they assume that the bigger animals have bigger brains, and therefore more intelligence. Either way, the results are usually quite amusing.
Granted, the same thing can happen to humans as well. The parrot-like thing riding on that humanoid's shoulder may actually be the master, with the humanoid being its mount. Or it might be that the spaceship itself is in charge, and the aliens disembarking are merely messengers.
Many parodies or humorous examples of the trope may include the revelation or implication that the lower animal actually is the dominant or superior species (at least in their own eyes).
See also Mistaken for Servant, which is a more mundane trope which sometimes overlaps.
- In Marvel's Transformers comics, the Autobots, having never encountered organic life before, initially believe vehicles to be the dominant lifeform on earth, which is why they use vehicles as alt modes. When Buster first meets Bumblebee, he's trying to communicate with the "locals" at a drive-through theatre.
- This also happened in Transformers Animated. See below.
- In one Mickey Mouse comic some aliens attempt to find if there is intelligent life on Earth and abduct Mickey and Pluto to perform tests on them. Pluto ends up scoring higher than Mickey, mostly because the tests are actually very simple and Mickey keeps overcompensating; for example, when the aliens attempt to translate their speech he speaks really slowly, causing the aliens to think he's stupid (while Pluto's barking confounds their Translator Microbes, making the aliens think Dog language is simply too complex for them to understand). The aliens end up concluding that dogs are the dominant species on Earth.
- In the film version of Battlefield Earth, the Psychlos interpret surveillance photos of humans with dogs in car passenger seats as evidence of the dogs being the superior species, since the humans "chauffeur them around".
- Good Boy! ultimately subverts this trope: The aliens in question are dogs, and they had sent some of their number to earth to colonize it and subjugate humanity in the first place, so the inevitable listing of the ways dogs are "really in charge" does occur. But Hubble, the dog sent to check up on their progress, is ultimately not impressed. And neither is his superior, who apparently had something more like total enslavement in mind.
- Star Trek the Motion Picture. V'Ger thinks that humans (including those on Earth) are "units" under the control of its Creator. The movie was based on the Star Trek the Original Series episode "The Changeling" where the robot Nomad believed the same thing.
- Basically the plot of Star Trek IV: The Voyage Home - the aliens think whales are/were the intelligent life on the Earth. Whether they even notice the humans swarming around on the dry parts is not clear.
- Carl Sagan gives an example in his book Pale Blue Dot, where aliens at first assume that cars are the main inhabitants of cities (the idea being that aliens would be taking closer and closer views of the earth while trying to find life, and cars are the first visible moving things they would see in city areas).
- Two human survivors in George Zebrowski's The Killing Star wind up getting captured by the alien invaders and have an audience with them. One wall of the room faces a water-filled chamber which contains an octopus-like creature being preened and taken care of by dozens of little robots. The captives assume that the creature is the brains behind the invasion when it begins speaking to them. It soon reveals, though, that the robots are in charge. They had been built by the octopi long ago and eventually surpassed them in intelligence. The octopi are considered by the masters to be more like a zoo exhibit of a curious precursor animal than anything else. And our two humans will ultimately share the same fate.
- Animorphs: During the What If Megamorphs 4, Back To Before, Ax briefly mentions mistaking cows for the dominant species, in this case because they're numerous and superficially similar to Andalites (who resemble centaurs).
- Harry Bates' story "Farewell to the Master" (which was later adapted into the movie The Day the Earth Stood Still) includes a viewpoint-reversed example that was not included in the film adaptation. The short story ends with the robot (named "Gnut" in the original) stating, "You misunderstand, I am the master."
- Ford Prefect of The Hitchhiker's Guide to the Galaxy uses his name because he believed that cars were the dominant species. To explain the joke to foreign audiences (because the Ford Prefect was only sold in England), the film adaptation shows that Arthur first met Ford when Ford stepped into the street to shake hands with an oncoming car (an actual Ford Prefect to boot) and Arthur saved his life by tackling him out of the way. 
- Star Trek Enterprise: Ferengis believe Porthos, Archer's dog, captains the Enterprise. They finally realize their mistake when their Universal Translator fails to work.
- Sesame Street martians tried to talk with a telephone. On the "bright" side, they repeated attempts with more than one Terran dictionary.
- In Destroy All Humans!, Crypto and Pox assume the first creatures they see - cows - are the dominant life form on Earth. An unsuccessful interview and some telekinetic stress relief later teaches them otherwise.
- In the first Space Rangers the main enemy - the klisans - are a race of biological starships. To be more precise, each member is a moon-size mothership, and all the smaller ships are its organs. They initially assume that the dominant species is the spaceships we fly in, and the humans in them are just a virus that makes them go insane. Thus, they seek to eliminate us in the same fashion we would try to kill an influenza, to prevent further infection and "cure" the infected vessels.
- In the final scenario of Hyperspeed, you make contact with two different aliens sitting in a tree and are prompted which to communicate with. No matter which you choose, it's the tree that talks back.
"What are you talking to my pet, [petname], for?"
- Luke Surl comics demonstrate what can happen if your main information sources for the First Contact are internet satellites.
- In Sequential Art Martian Trashcans arc, "Gary" tried to talk with two inanimate objects in a row. He apparently isn't the brightest bulb in his team, considering he's the one habitually sent to collect cow lips while others tend to their little military business.
- What on Earth, an old Canadian cartoon by Kaj Pindal which purports to be an educational film by Martians, who looked down on the earth and naturally assumed that cars were the dominant life-form, and humans some kind of parasite they hadn't gotten around to ridding themselves of.
- In South Park the aliens have fully researched the planet and decided that cows were the most intelligent species. If they were only looking at the adults, they are probably right.
- War Planets features an example. A race of humanoids apparently uses a race of furry, wookiee-like creatures as draft animals. The main characters assume the smaller humanoids are the dominant species, when in fact it is the "draft animals" who are both smarter, and telepathic.
- On Garfield and Friends an alien crash lands near Garfield's house. He believes that Jon is Garfield's servant and that Garfield is the planet's superior intelligence.
- An episode of Dennis the Menace featured an alien race of shape shifters who thought that telvisions ruled the world and thus came to Earth in the form of televisions. Upon realising their mistake they tried to take on human form but found it too difficult so remained as televisions. At the end, they revealed their true forms (each one different from the rest) and concluded they were just like humans in that regard.
- In Transformers Animated, when the Autobots first arrive they disguise themselves as "the dominant life forms." Bulkhead attempts to chat up a robot dog while the Autobots help fight a monster, only to find out that the organic creatures running around aren't "pets"; robots and vehicles aren't sentient, and humans are the dominant life.
- The Decepticons don't fare much better. When Blitzwing and Lugnut arrive on Earth they initially mistake vehicles for lifeforms, to the point of getting into a fight with a crane.
- While it's not obvious at first, even humans aren't the dominant species on Earth. In fact, we're only the third most intelligent species on the planet, after mice and dolphins.