Despite increasing representation in graduate training programs, a disproportionate number of women leave academic research before obtaining an independent position. To understand factors underlying this trend, we analyzed a multidisciplinary database of Ph.D. and postdoctoral mentoring relationships covering the years 2000-2020, focusing on data from the life sciences. Student and mentor gender are both associated with differences in rates of student's continuation to independent mentor positions of their own. Although trainees of women mentors are less likely to take on independent positions than trainees of men mentors, this effect is reduced substantially after controlling for several measurements of mentor status. Thus the effect of mentor gender can be explained at least partially by gender disparities in social and financial resources available to mentors. Because trainees and mentors tend to be of the same gender, this association between mentor gender and academic continuation disproportionately impacts women trainees. On average, gender homophily in graduate training is unrelated to mentor status. A notable exception to this trend is the special case of scientists having been granted an outstanding distinction, evidenced by membership in the National Academy of Sciences, being a grantee of the Howard Hughes Medical Institute, or having been awarded the Nobel Prize. This group of mentors trains men graduate students at higher rates than their most successful colleagues. These results suggest that, in addition to other factors that limit career choices for women trainees, gender inequities in mentors' access to resources and prestige contribute to women's attrition from independent research positions.