Variation and disparity within the inner ear and trigeminus of the Tenrecomorpha
Data files
Jul 01, 2025 version files 104.02 MB
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Dryad_Data.zip
104.02 MB
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README.md
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Abstract
How does the evolution of specialized sensory systems relate to adaptive radiation? Does adaptation to different ecological niches correlate significantly with changes in sensory anatomy? The afrotherian clade Tenrecomorpha, represented today by the African potamogalines and the Malagasy tenrecines, is of particular interest in this regard because of its extraordinary variety: its membership reportedly includes fossorial, arboreal, semiaquatic, and even echolocating taxa. To investigate their sensory ecology further, here we provide geometric morphometric analyses of inner ear endocasts (i.e., the bony labyrinth) of 24 tenrec species. We expand this data set with iodine-stained specimens of an additional 9 species, to provide information on cerebral and trigeminal organization. Although tenrecomorphs display cross-taxon differences in structures that may relate to sensory ecotype, our analyses distinguish signals of conflicting strength and direction within the tenrec ear. We found no single factor that might explain a substantial portion of the observed variation when controlling for phylogenetic signal. This is in marked contrast to prior studies of the tenrec cranial endocast, where sensory ecotype and habitat are more strongly associated with shape change. Iodine-enhanced scans of the trigeminal nerve are nonetheless consistent with this and other studies based on bony anatomy. The disparate patterns of shape evolution within the Tenrecomorpha and the contrasting signals of variation exhibited by the inner ear and trigeminal nerve provide a nuanced portrait of neurosensory adaptation and a departure from expectations set by other mammalian groups.
https://doi.org/10.5061/dryad.4qrfj6qjn
This dataset contains the code and raw landmark data needed to recreate the analyses in this paper.
We have submitted the raw landmark data (including Curved_Landmarks and Fixed_Landmarks) models of of the inner ear bony labyrynth (Inner_Ears) in addition to the data files for running analyses: a trimmed phylognetic tree (tenrec_pruned.tre), categorical data (Table_S1_Tenrec_Categories) measurements from the trigeminal nerve (Table S3 Traw_Trigeminal_Data) and R code required to recreate the analyses in this paper (Code_Resubmission_Final)
Description of the data and file structure
Included are three folders:
Curved_Landmarks: This folder contains the unadjusted semilandmark curves for each specimen, saved as JSON files. The specimen name for each is located in the filename.
Fixed_Landmarks: This folder contains the unadjusted landmarks for each specimen, saved as JSON files. The specimen name for each is located in the filename.
Inner_Ears: This folder contains the mesh .PLY files of all inner ear models used for this study, rendered via 3DSlicer (see manuscript for additional details). The specimen name for each is located in the filename. Almost all meshes are based on the left side of each specimen; where this was not possible, a right ear was used and mirrored prior to analyses and is indicated in the name of the file.
Table_S1_Tenrec_Categories.csv: a .csv file that includes:
- Taxon: Currently valid scientific name
- Family: Family name, after Everson et al (2016)
- Subfamily: Subfamily name, after Everson et al (2016)
- Genus: Genus name, after Everson et al (2016)
- Subfamily: Subfamily name, after Everson et al (2016)
- Locomotion: Locomotor category
- Ecomorph: Sensory ecomorphotype
- Habitat: Habitat type, after Everson et al (2016)
- Diet (complex): Diet, including specific categories of prey items (for example, aquatic prey is divided between fish and aquatic insects)
- Diet (simple): Diet, without specific categories of prey items (for example, fish and aquatic insects are grouped as "aquatic prey")
- Diet Citation: Literature reference for dietary assignment
- Diet Citation: Literature reference for dietary assignment
- Specimen: Museum accession ID for each Specimen
- Body_Mass_Grams: Body mass (g)
- Body_Mass Citation: Citation for Body Mass assignment
- PCA_Numnbers: Reference for plotting (see manuscript for additional details)
Table S3 Traw_Trigeminal_Data.csv: a .csv file that includes:
- Taxon: Currently valid scientific name
- Foramen Magnum cm2: Cross-sectional area of the Foramen Magnum (cm^2)
- Infraorbital L cm2: Cross-sectional area of the left Infraorbital foramen (cm^2)
- Infraorbital R cm2: Cross-sectional area of the right Infraorbital foramen (cm^2)
- Trigeminal L cm2: Cross-sectional area of the left trigeminal (==infraorbital) nerve as it passes through the infraorbital foramen (cm^2)
- Trigeminal R cm2: Cross-sectional area of the right trigeminal (==infraorbital) nerve as it passes through the infraorbital foramen (cm^2)
- L Fill Ratio (Trig/IOF): Ratio of the area of the trigeminal nerve/area of the infraorbital foramen on the left side
- R Fill Ratio (Trig/IOF): Ratio of the area of the trigeminal nerve/area of the infraorbital foramen on the right side
- Avg Fill Ratio: Average fill ratio between right and left sides
- Avg IF: Average infraorbital cross-sectional area between right and left sides
- Avg Trig: Average trigeminal cross-sectional area between right and left sides
- Centroid Size: Size of the skull centroid
- Body Mass (g) -PanTHERIA: Body mass (g) from the panTHERIA database
tenrec_pruned.tre: Phylogenetic tree of tenrec taxa from Everson et al (2016), pruned to only include the taxa included in this study.
Key Information Sources
As cited in these files and in the main text of the manuscript, much of the body mass data is sourced from the PanTHERIA database.
Code/Software
R is required to run Code_Resubmission_Final.r; all necessary libraries are specified within the code itself. All code was run in R 4.4.1, and annotations are provided in the script.
Skulls of 24 tenrecomorph species were scanned on the GE Phoenix Vtome x SMicroCT scanner in the AMNH Microscopy and Imaging Facility (MIF), at a target resolution between 18-56 μm. For all taxa, the left bony labyrinth of adult specimens was segmented. For 4 specimens where this structure was damaged or otherwise unsuitable for analysis, the right cochlea was segmented and mirrored prior to analysis. For rendering, specimens were reconstructed with the 3DSlicer software suite and semilandmarks placed using the SlicerMorph package. For fixed landmarks, landmarks were collected, translated from a template (Nesogale talazaci) using the ALPACA module, and corrected/resampled by hand where necessary. Cochlear and semicircular landmarks were placed and resampled manually for each specimen, and all landmarks were merged to form the final dataset.