These files provide the raw data necessary to repeat the analyses presented in Sloan & Simmons, Divergence in the internal genital morphology of females correlated with divergence in male intromittent structures among populations of a millipede. Evolution, 2023. IDs Individuals are labelled by their geographic origin: Gingin, Avon Valley, Nalya Park, Kings Park (both KPJ and Thomas Road), Ellis Brook, Beeliar and Serpentine (e.g. Avon1\_m is male 1 collected from Avon valley. Morphology PLY (polygon file format) files are the surface mesh files extracted from Avizo v9.2.0. Each .ply file contains the 3D scan data (x, y, z coordinates) that describe the surface mesh for each male gonopod and each female receptaculum. These files can be entered into the Generalized Procrustes Surface Analysis (GPSA) software available in Pomidor et al. (2016) to reproduce the shape variables provided in the gpsa\_ordination\_projection files. The .ply files can also be opened in any graphics package to visualize the surface mesh for each individual. The gpsa\_ordination files contain the data used in downstream analyses. The columns, Axis1 – Axis*i* are the scores of each individual on the first to ith major axis from the principal coordinates analysis. Collum area is also provided for each individual. Genetics Two files are provided; the raw SNP data from DArT, and the set of neutral SNP loci following outlier detection. Cells in this file containing NA represent SNPs that could not be scored. Pomidor B.J., Makedonska J., Slice D.E. 2016 A landmark-free method for three-dimensional shape analysis. *PLOS ONE* **11**(3), e0150368. (doi:10.1371/journal.pone.0150368).

Our understanding of genital evolution comes largely from studies of male genitalia. Females have received far less attention because of the difficulties inherent in quantifying the shapes of their internal genital structures. Here we combine advances in micro-computed tomography with a new landmark free method of quantifying three-dimensional trait shape, to document patterns of divergence in female genital shape, and the correlated divergence of male genitalia among populations of the millipede Antichiropus variabilis. We used single nucleotide polymorphisms to estimate levels of neutral genetic divergence among seven populations of millipede. Genetic divergence was high and correlated with geographic distance. Comparing phenotypic divergence in genital shape to neutral genetic divergence, we found that genital shape for both females and males has diverged more than would be expected from random drift, consistent with a pattern of directional selection. While there was significant covariation between female and male genital shape across populations, the magnitude of divergence in genital shape between the sexes was not correlated. Our results demonstrate the utility of using three-dimensional scanning technologies to examine female genital traits and add to a small but growing number of studies showing that like male genitalia, female genitalia can be under strong directional selection.

Millipedes collected from the field, stained and scanned using micro-CT. Surface meshes used in GPSA to extract 3D shape data for downstream statistical analyses. DNA sequences and neutral SNPs identified for analysis of population genemtic parameters.