The article uses terms that are known to biologists which can be easily searched for.

There are genes called "selfish genes" which cause a negative impact on the organism. Normally they would be selected out by evolution, but the "selfish" part means the gene is propagated to descendant organisms far more often than a regular gene would be. There are several mechanisms that can cause this, wikipedia has a summary.

In this case the ants have a "selfish gene" which greatly increases the probability of an egg being a queen, which makes it much harder for the colony to thrive.

As for the mixing of the species? You'd need a time travel machine to find out for sure, but the researchers noted that the species live in proximity and do mate together when in the same area. This would allow the queen to produce the needed workers. Evolution drove forward and somehow created a mechanism that allowed the ants to maintain the DNA required independent from the origin species. That's what the researchers are looking for now.