Using the corpus of JSTOR articles, we investigate the role of gender in collaboration patterns across the scholarly landscape by analyzing gender-based homophily--the tendency for researchers to co-author with individuals of the same gender. For a nuanced analysis of gender homophily, we develop methodology necessitated by the fact that the data comprises heterogeneous sub-disciplines and that not all authorships are exchangeable. In particular, we distinguish three components of gender homophily in collaborations: a structural component that is due to demographics and (...) non-gendered authorship norms of a scholarly community, a compositional component which is driven by varying gender representation across sub-disciplines, and a behavioral component which we define as the remainder of observed homophily after its structural and compositional components have been taken into account. Using minimal modeling assumptions, we measure and test for behavioral homophily. We find that significant behavioral homophily can be detected across the JSTOR corpus and show that this finding is robust to missing gender indicators in our data. In a secondary analysis, we show that the proportion of female representation in a field is positively associated with significant behavioral homophily. (shrink)