It is the first study to link supergenes to animal behaviour, the scientists reported in the journal Nature, and predicted a similar effect would be found in other species.
Native to South America, the red fire ant organises itself into two distinct types of social structure - one with a single queen per colony, the other with hundreds.
Though they are the same type of ant, the workers of either group would kill the queens of the other, the international researchers wrote.
The two groups also differ physiologically: one produces large queens which accumulate a lot of fat and fly away to start new colonies, where they feed their first larvae from their body reserves.
The other group yields smaller queens that remain in an established colony with existing workers and other queens.
Scientists have previously identified a gene variation between the two groups, but have been at a loss to explain how a single gene change could yield so many social and physiological differences.
"People had speculated it could be a supergene, and now that has been confirmed," biologist Andrew Bourke of the University of East Anglia told AFP in a comment on the paper.
"There are other cases known where supergenes affect complex traits. But this is the first case where a supergene is shown to underpin complex social behaviour... in any animal."
A supergene is a grouping of neighbouring genes on a chromosome that somehow become fused together and are then passed on, unchanged, from generation to generation.
In this case, the team found two variants of a supergene on a pair of ant chromosomes, comprising more than 600 genes or nearly 60 percent of the chromosome.
"This is the first description of a social chromosome," wrote the authors, "yet it is likely that such supergenes affecting social organisation also exist in other social insects."
As far as human beings are concerned, there is no evidence to date that supergenes are in any way involved in our social organisation, Bourke said.
The red fire ant has become a pest in the southern United States, China and Australia. It's Latin name, Solenopsis invicta, means "the invincible."
Lead author Laurent Keller told AFP the findings may one day be useful in combating the ants.
It could, for example, lead to the manufacture of a chemical containing a synthetic version of that part of the supergene that tells workers to kill rival queens, turning them on their own instead and so ending the colony.