Background: Brains are complicated. We don't have an "autism gene" or a "smart gene" or a "schizophrenia gene." Rather, it is a network of genes acting in concert that give rise to these traits (autism, smart, schizophrenia, etc).

The researchers looked at the genes that are involved in autism - certain "alleles" (versions of a gene) are correlated with autism.

They were surprised to find that several of these autism-related alleles were also associated with increased intelligence. That is, having one or more "autism-like" alleles may boost your intelligence, without necessarily causing autism.

They then looked at the prevalence of these autism-related alleles, and found that it was significantly higher than you would expect to see by random chance. From this, they can conclude that there is positive selection occurring - having at least one autism-related allele results in you being more likely to pass your genetics on to your children.

I may be missing a few things; I read the paper pretty quickly.