Data from: Testing for functional adaptation in a genital bone: Baculum size, shape, and microstructure do not respond plastically to recurrent mating
Data files
Sep 10, 2026 version files 139.29 MB
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dryad_archive.zip
139.28 MB
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README.md
9.57 KB
Abstract
Plasticity – the ability of a genotype to produce different phenotypes in response to environmental input – can be used to infer the mechanical forces experienced by biological structures. Bones are quintessentially plastic, remodeling in response to compression and torsion. The males of many mammal species possess a bone in their penis called a baculum. Across species, its extreme morphological divergence suggests it undergoes recurrent adaptive evolution, and several studies have explicitly linked baculum size and shape to reproductive fitness. However, the precise functions of this bone remain largely unknown. Here we test whether copulation imposes mechanical loading sufficient to induce remodeling in the baculum. We compared bacula of mated vs. unmated males in two different rodent lineages with divergent baculum morphologies and mating ecologies, using high-resolution morphometric and synchrotron-enabled quantification of bone microstructure. We found no consistent differences in size, shape, or microstructure between bacula of mated versus unmated males. These results suggest that the baculum is not subject to mechanical loads strong enough to induce remodelling, and that its rapid evolutionary divergence is not enabled by load-induced plasticity.
Description of the data and file structure
Dataset overview
This dataset accompanies a study testing whether mating induces plastic changes in baculum size, shape, or bone microstructure. It contains specimen metadata, cleaned three-dimensional baculum surface meshes derived from microCT scans, output from landmark-free GPSA2 morphometric analyses, and synchrotron-derived measurements from six house-mouse bacula. The study includes a primary house-mouse experiment, a reanalysis of a previously published house-mouse dataset, and four Peromyscus species.
The deposited PLY files are processed surface meshes rather than the original microCT image stacks or raw synchrotron projections.
Abbreviations
MUS: primary C57BL/6J house-mouse experimentMUS_SCHULTZ: house-mouse data from Schultz (2019), reanalyzed for this studyBW: Peromyscus maniculatus bairdiiIS: Peromyscus californicus insignisLL: Peromyscus leucopusPO: Peromyscus polionotus subgriseus
File structure and descriptions
The deposited wrapper ZIP contains:
README.md: this file.dryad_archive.zip: the substantive data archive described below.
dryad_archive.zip
dryad_archive/sychrotron_data/
The directory name is spelled sychrotron_data in the archive.
synchrotron_data.xlsx: synchrotron radiation-based microCT measurements for six house-mouse specimens from the mating treatment (12935,12936, and12937) and the individually housed unmated treatment (12941,12942, and12943). The workbook contains three sheets:Biomechanical Data: one row per specimen, with the analyzed slice number and cross-sectional/geometric measurements, including cross-sectional area, centroids, density, radii, area moments of inertia, section moduli, Feret diameters, perimeter, and 2D/3D thickness measurements. Units are included in the column headings.Structural Data: specimen-specific 2D and 3D structural measurements in a wide layout. Measurements include pore volume and surface area, pore surface-area-to-volume ratio, structure model index, pore thickness, pore number, pore separation, number of pores, anisotropy, bone volume and surface area, percent bone and pore volume, pore surface density, and related 2D measures. The sheet includes formulas converting pixel-based measurements to micrometer-based units using a 1.5 micrometer pixel size. There are some gray boxes in Structural Data - they simply indicate cells that are supposed to be blank. For example, "degree of anisotropy" is grayed out for labeling units because it is a unitless measurement.data_wrangled_by_matt: the structural measurements reorganized into a long, analysis-oriented table with specimen, analysis dimensionality (2D or 3D), measurement name, abbreviation, value, and unit/conversion fields.
dryad_archive/plyfiles/
This directory contains the cleaned baculum surface meshes used as input to GPSA2, plus spreadsheets connecting specimen identifiers to treatment or breeding status. Meshes are Polygon File Format (.ply) files bundled into compressed tar archives (.tar.gz).
MUS/MUS.tar.gz: 12 baculum surface meshes from the primary C57BL/6J house-mouse experiment.specimens.xlsx: lookup table relating each male identifier to one of four treatments: mating, unmated plus female bedding, unmated alone, or unmated caged together.
MUS_SCHULTZ/MUS_SCHULTZ.tar.gz: 21 baculum surface meshes from the Schultz (2019) house-mouse dataset reanalyzed in the paper.specimens.xlsx: lookup table containing specimen name, quartet number, and mated/unmated status.
PEROMYSCUS/peromyscus_specimens.xlsx: specimen metadata for the 16 Peromyscus bacula (four per species). Columns record dissection date, species, strain abbreviation, specimen ID, breeder/virgin status, number of litters, body mass, body dimensions, and reproductive-organ measurements. Measurement units are not specified in the workbook's column headings.BW/PEROMYSCUS_BW.tar.gz: four surface meshes for P. maniculatus bairdii.IS/PEROMYSCUS_IS.tar.gz: four surface meshes for P. californicus insignis.LL/PEROMYSCUS_LL.tar.gz: four surface meshes for P. leucopus.PO/PEROMYSCUS_PO.tar.gz: four surface meshes for P. polionotus subgriseus.
dryad_archive/GPSA2_results/
This directory contains the complete GPSA2 output for each independently analyzed group. GPSA2 iteratively homologizes and superimposes surface meshes and produces size estimates and principal-component ordinations of shape.
MUS/analysis_results_20221029_110401.tar.gz: GPSA2 results for the 12 specimens in the primary house-mouse experiment.MUS_SCHULTZ/analysis_results_20260319_045621.tar.gz: GPSA2 results for the 21 specimens in the Schultz (2019) house-mouse dataset.PEROMYSCUS/BW/analysis_results_20260306_123840.tar.gzGPSA2 results for the four P. maniculatus bairdii specimens.PEROMYSCUS/IS/analysis_results_20260306_124119.tar.gzGPSA2 results for the four P. californicus insignis specimens.PEROMYSCUS/LL/analysis_results_20260306_124356.tar.gz: GPSA2 results for the four P. leucopus specimens.PEROMYSCUS/PO/analysis_results_20260306_124549.tar.gz: GPSA2 results for the four P. polionotus subgriseus specimens.
Each GPSA2 results archive contains most or all of the following output types:
*_homologized.ply: specimen meshes restricted to homologous surface regions identified by GPSA2.*_superimposed.ply: aligned specimen meshes after GPSA2 superimposition.ordination_*.ply: reconstructed meshes representing positions along principal-component axes; filenames encode the ordination axis and projection magnitude.prototype_*_pre-smooth.plyandprototype_*_post-smooth.ply: prototype meshes before and after smoothing during GPSA2 processing.mean.ply: mean surface mesh.varianceMap.ply: surface mesh containing the spatial variance map.labels.txt: specimen labels in the order used in the numerical outputs.ordination_projections.txt: specimen scores/projections in ordination space.ordination_values.txt: numerical values associated with the ordination axes.size_estim_sample.txt: surface-area-weighted centroid-size estimate for each specimen.size_estim_mean.txt: centroid-size estimate for the mean surface.homologized_points.txt: coordinates of homologized surface points.sample-homologized_distance.txtandsample-mean_distance.txt: distances between each specimen and the homologized or mean surface.homologized-mean_distance.txt: distances between the homologized and mean surfaces.interspecimen_distance-homologized_sample.txtandinterspecimen_distance-superimposed_sample.txt: pairwise interspecimen distance matrices based on homologized or superimposed meshes.prototype_distance_per_iteration.txt: prototype-surface distance across iterations, useful for assessing convergence.saved_par3d.txt: saved 3D viewing parameters; present in the Peromyscus result archives.console.log: GPSA2 configuration and processing log; present in the primaryMUSresult archive.
Important identifier note
In plyfiles/PEROMYSCUS/peromyscus_specimens.xlsx, one P. leucopus specimen is recorded as LL.24277. The corresponding input surface mesh and GPSA2 output files are named LL.24227. These appear to refer to the same specimen; users joining the spreadsheet to mesh-derived results should account for this identifier discrepancy.
Within MUS_SCHULTZ, some specimen identifiers in specimens.xlsx omit the leading B_ that appears in the corresponding PLY filenames.
Non-data system files
The ZIP and some enclosed tar archives contain macOS-generated files or directories such as .DS_Store, __MACOSX/, and files beginning ._. These contain Finder metadata or resource forks and can be ignored; they are not research data.
Sharing/Access information
The dataset is publicly available from the Dryad Digital Repository at https://doi.org/10.5061/dryad.jm63xsjrp.
Related publication: Toney, C. F., Schultz, N. G., Pomidor, B., Taylor, J., Andronowski, J., and Dean, M. D. (2026). Testing for Functional Adaptation in a Genital Bone: Baculum Size, Shape, and Microstructure Show Little Plastic Response to Mating Across Five Rodent Species. Integrative Organismal Biology, obag043. https://doi.org/10.1093/iob/obag043
No access restrictions apply to the deposited data.
Code/Software
File formats
.xlsx: Microsoft Excel workbooks; readable with Excel, LibreOffice, R, Python, or other spreadsheet software..ply: three-dimensional Polygon File Format surface meshes; readable with MeshLab and many other 3D-mesh programs..tar.gz: gzip-compressed tar archives; extract with standard archive utilities before use..txtand.log: plain-text GPSA2 numerical output and processing logs.
Software
The analyses described in the paper used Slicer3D for segmentation and surface extraction, MeshLab/pymeshlab for mesh processing, GPSA2 for morphometric homologization and superimposition, ORS Dragonfly for synchrotron-image segmentation, and R for statistical analyses. Analysis scripts are not included in this deposit.
