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Quantification of genital variation in males and females can inform our understanding of likely copulatory interactions and evolution of genital diversity. However, no studies have quantified genital shape variation within a single snake species or examined the shape and size of both the vaginal pouch and hemipenes. Here, we examine the shape and size of the genitalia of female and male diamondback water snakes, Nerodia rhombifer, using a three-dimensional automated landmark geometric morphometric approach on models of the lumen of the vaginal pouch and inflated hemipenes, applying these techniques for the first time to the genital shape of vertebrates. Vaginal pouch shape is significantly associated with body size and reproductive status. As females grow larger and become reproductive, the vaginal pouch enlarges, widens and becomes more bifurcated. In reproductive males, the shape of the hemipenes is also significantly associated with body size. As males grow larger, the hemipenes enlarge and widen; their bifurcation becomes more defined and the spines at the base become more prominent. Vaginal pouch and hemipenial centroid size are isometric with respect to body length. The centroid sizes of the hemipenes and vaginal pouch are not significantly different from one another, hence the genitalia match in size. Reproductive females and males covary in the degree of bifurcation and size of their genitalia. We demonstrate the utility of three-dimensional analysis in studies of the shape of soft tissues and advocate its use in future studies of genitalia.

Genital evolution can be driven by diverse selective pressures. Across taxa we see evidence of covariation between males and females, as well as divergent genital morphologies between closely related species. Quantitative analyses of morphological changes in coevolving male and female genitalia have not yet been shown in vertebrates. This study uses 2D and 3D geometric morphometrics to quantitatively compare the complex shapes of vaginal pouches and hemipenes across three species of watersnakes (the sister taxa Nerodia fasciata, N. sipedon, and a close relative N. rhombifer) to address the relationship between genital morphology and divergence time in a system where sexual conflict may have driven sexually antagonistic coevolution of genital traits. Our pairwise comparisons of shape differences across species show that the sister species have male and female genitalia that are significantly different from each other, but more similar to each other than to N. rhombifer. We also determine that the main axes of shape variation are the same for males and females, with changes that relate to deeper bilobation of the vaginal pouch and hemipenes. In males, the protrusion of the region of spines at the base of the hemipene trades off with the degree of bilobation, suggesting amelioration of sexual conflict, perhaps driven by changes in the relative size of the entrance of the vaginal pouch that could have made spines less effective.