By studying males only, mostly male scientists believed they could more easily identify the most basic ways the brain worked without the “messiness” of fluctuating female hormones. This stereotype is so pervasive that some biomedical researchers still don’t question why they aren’t looking at female rats or mice.

It also set up men as the norm. “We live in a world where the assumption is that males are the standard, the reference population, and females are the ones that are odd,” said Daniela Pollak, a neurobiologist who wrote an essay on the problem earlier this year.

In recent years, analyses of hundreds of neuroscience studies offered clear evidence disproving the idea that males are less hormonal. In some cases, male rodents living in groups were messier because their testosterone (which essentially works on the brain like estrogen) fluctuates, depending on dominance hierarchies in groups.

That males were hormonal, emotional and messy still didn’t get them kicked out of studies.

Even if scientists had shown that females were more complex subjects, “it would not suffice as an excuse,” said Dr. Pollak. “Scientists are not meant to give up on a problem just because it starts becoming complicated.”

Encouraged by the N.I.H. and Canadian mandates, scientists are reconsidering the effects of sex in their research. But this may not be enough to improve the outcomes if it primarily results in researchers just using more female subjects without understanding all the ways stereotypes influence animal studies.

Dr. Shansky offered an example of how females were expected to behave in tasks designed to model post-traumatic stress in male rodents. Instead of freezing as males did, the females darted around during experimental tests. Without recognizing this behavior as different, rather than wrong, one might say females failed the task.

“We’ve gone from excluding women and female animals to this ham-handed implementation of sex as biological variable,” said Ann Fink, a feminist neuroscientist and gender scholar at Lehigh University.