What is the gender gap like in upper level sciences, first hand?

It is actually quite staggering and to be completely honest a bit disheartening and discouraging. Don't let that stop you though because as a minority multi racial student from a disadvantaged socio-economic background I never gave up even though I faced prejudice. For example, I faced difficulties with the department of chemistry under which I earned my degree specifically with slanderous information being spread around and levied upon me which directly affected my GPA. I directly observed unfair practices in grading regarding tests, quizzes, and assignments which I confirmed by comparing my work and how it was graded with other student's work with largely the same exact answers or content being downgraded while theirs got full or near full credit for the exam problem or the laboratory reports. You should do it anyway because how else will things change for underrepresented student groups?

I can't answer for people entering mathematics today, but I know in veterinary medicine and horticultural and agricultural plant breeding, it's shifted and there are now more female graduate students than males in many Universities. And I do know that most academic and research places in the USA and Europe care more about your professionalism and work performance.

After personally living and working in two isolated pockets in the past where folks knew that I "wasn't from around there" (and I'm a white male), I'd advise going to school and working at larger Universities or places where issues related to gender or even just not being from around there, are less likely come up. If an issue like that does come up, it's easier to take it up with HR in a larger University or other environment, than in an isolated pocket of the US.