DOI: 10.5061/dryad.nvx0k6f0f
title: Allometry of bony sound reception structures

description: The origin of sensory structures provides an excellent framework for
 studying how constraints and selective pressures affect the evolution of
 complex features. The evolution of the mammalian middle ear from the jaw
 hinge of non-mammalian synapsids offers a deep time perspective on sensory
 evolution but is limited by a poor understanding of early synapsid
 hearing. This work tests hypothesis that the reflected lamina of the
 angular in non-mammalian synapsids followed a strict, negative allometric
 trend that may be expected for a sound reception structure. Allometry is
 first investigated in the pterygoid of chameleons, which was co-opted for
 hearing in some species and represents a possible analog for the synapsid
 reflected lamina. Results indicate that chameleons with a pterygoid ear
 converge on a similar allometric slope, while other species have variable
 slopes, suggesting an optimum allometric pattern in sound receivers. In
 the reflected lamina, we find reduced variation around the allometric
 trend in therocephalians and non-bidentalian anomodonts, and evolutionary
 modeling suggests constraint in these groups. These results are consistent
 with a mandibular middle ear in non-mammalian synapsids, suggesting that
 selective pressures for hearing ability were present long before the
 evolution of the mammalian middle ear.
description: We photographed museum specimens of chameleons in ventral,
 lateral, and ventromedial views, and synapsids were photographed in
 lateral view with a Nikon D3100 camera. Additional photographs of
 inaccessible synapsid specimens were graciously provided by other
 researchers and museum staff. 59 synapsid specimens were also 3D surface
 scanned using an Artec Space Spider blue light scanner with a voxel size
 of 0.3 mm. For chameleons, ImageJ V1.51j (Schneider et
 al., 2012) was used to measure basal skull length, pterygoid plate area,
 orbit diameter, and coronoid process height from photographs. In
 synapsids, we measured reflected lamina area in ImageJ and mandible length
 and orbit diameter using a Neiko digital caliper. Area was measured by
 outlining each structure with the “polygons selection” tool in ImageJ.
 When photographs and/or caliper measurements were unavailable, comparable
 measurements were taken using Meshmixer V3.5.474 (©Autodesk, San Rafael,
 CA, U.S.A) and the R package molaR (Pampush et al., 2016) on 3D surface
 scans.
description: # Allometry of bony sound reception structures Dataset DOI:
 [10.5061/dryad.nvx0k6f0f](10.5061/dryad.nvx0k6f0f) ## Description of the
 data and file structure Data on the allometric scaling of the pterygoid
 plate of chameleons with basal skull length, as well as the reflected
 lamina of the angular in synapsids with jaw length. Please note that most
 of these are raw data files that were not directly input to our analysis.
 The files that were reorganized for more direct use in our analyses can be
 found along with our code on our Github repository at
 [https://github.com/savannaholroyd/EarBoneAllometry](https://github.com/savannaholroyd/EarBoneAllometry). ### Files and variables #### On Zenodo - Supplemental Information The images included with the dataset illustrate how measurements were taken, and the "Supplementary information" pdf file provides details about how measurements were taken, which institutions the specimens were housed in, and how missing data was estimated. It also includes captions for all of the images provided, as well as some supplemental data analysis results. **File: Supp_data_1.csv** **Description:** Replicate measurements of pterygoid plate area for estimation of measurement error **Variables** * Specimen #: Museum collection code and number. Abbreviations can be found in the supplemental information for the paper. * Species: Genus and species name * Pterygoid plate area (mm^2) 1st measurement: First replicate measurement of pterygoid plate area. Measurement was done by selecting the pterygoid plate in images with ImageJ. We repeated this process three times and found the standard error between the three sets of measurements to get an estimate of measurement error. * Pterygoid plate area (mm^2) 2nd measurement: Second replicate, as described above. * Pterygoid plate area (mm^2) 3rd measurement: Third replicate, as described above. Note that some specimens were not measured a third time due to time constraints. #### On Dryad **File: Supp_data_2.xlsx** **Description:** Measurements of skull and jaw features of synapsids (units in file). Many specimens were incomplete, so measurements were estimated using methods described in the supplementary document for our paper. Each raw measurement or estimated measurement has its own column, and an “NA” in a column denotes that this measurement or estimate was not taken for that specimen. Raw measurements were copy-pasted to the spreadsheet “DataSynOUready.csv” in our GitHub repository for specimens that could be directly measured, and the estimated measurements were copied over for the other specimens. The sheet provided on Dryad is not what was used directly in the analysis; it was simply used to keep track of where the different measurements for each specimen came from. Detailed descriptions of how all measurements were taken or estimated, including example photos, can be found in the supplemental document for our paper.  **Variables** * Specimen #: Museum collection code and number. Abbreviations can be found in the supplemental information for the paper. * Species: Genus and species name * Clade: Broader clade that the species belongs to within Synapsida. These designations were used to subdivide the dataset to look for broad trends across Synapsida as well as trends within the individual clades. * Jaw length from photo: Length of the lower jaw as measured from a photo in ImageJ. We considered this an indirect measurement used only when calipers could not be used on a specimen. * Reflected lamina area from photo: Area of the reflected lamina as measured from a photograph by selecting the entire surface in ImageJ. We considered this the most direct measurement of reflected lamina area, so the values from this column were copied to the analysis files when available. * Jaw length from scan: Length of the lower jaw measured on a surface scan in Meshmixer. We considered this an indirect measurement used only when calipers could not be used and a photo was not available. * Reflected lamina area from scan: Area of the reflected lamina as measured from a surface scan using molar. We considered this an indirect measurement only used when a photo was not available. * Basal skull length from calipers: Length of the skull from the occipital condyle to the snout, measured with calipers. Our analysis used lower jaw length to represent head size, so basal skull length was only used to estimate jaw length when the jaw was too incomplete to get a measurement from. * Jaw length from calipers: Length of the jaw as measured with calipers. We considered this the most direct measurement of jaw length, so the values from this column were copied to the analysis files when available. * Estimated caliper jaw length: Using regressions described in full in the supplemental document, we estimated what the jaw length measured from calipers would be for specimens for which we could not get a caliper measurement. This was done using the measurements we were able to take. * Estimated photo reflected lamina area: Using regressions described in full in the supplemental document, we estimated what the reflected lamina area measured from photos using ImageJ would be for specimens for which photos were unavailable. This was done using the measurements we were able to take. * Orbit diameter: Diameter of the orbit, measured with calipers. Many specimens did not preserve both the orbit and the lower jaw, so this measurement is not available for all specimens. We used this measurement to look at trends in orbit allometry among synapsids for comparison with the trends we saw in the reflected lamina allometry. * Coronoid height: Height of the coronoid process or eminence, measured with calipers. Some specimens lacked this portion of the jaw, so this measurement is not available for all specimens. We used this measurement to look at trends in coronoid allometry among synapsids for comparison with the trends we saw in the reflected lamina allometry. **File: Supp_data_3.csv** **Description:** Log-transformed measurements of chameleon skull length, pterygoid area, orbit diameter, and coronoid height. A simplified version of this dataset for analysis can be found on our GitHub repository under the file name “masterAll.csv” **Variables** * Function: Whether or not the pterygoid functions as an ear in each species. “Non” means the pterygoid is not used for hearing, “Hearing” means the pterygoid is used for hearing. * Species: Abbreviated genus initial and species name. These were simplified versions of each species name used in the analysis. * Specimen #: Museum collection code and number. Abbreviations can be found in the supplemental information for the paper. * Sex: The identifiable sex of each specimen. NAs denote lack of information on the sex of the specimen. * Logbsl: Log-transformed measurement of basal skull length, measured from the tip of the snout to the occipital condyle. * Logpter: Log-transformed measurement of the area of the pterygoid plate, measured from photos using ImageJ. * Logorb: Log-transformed measurement of orbit diameter. * Logcor: Log-transformed measurement of coronoid process height. ## Code/software All the data provided here is in .csv format and can be viewed using software such as Microsoft Excel, Google Sheets, text editors, etc. Please note that most of these are raw data files that were not directly input into our analysis. The files that were reorganized for more direct use in our analyses can be found along with our code on our Github repository at [https://github.com/savannaholroyd/EarBoneAllometry](https://github.com/savannaholroyd/EarBoneAllometry). ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * Measurements taken from specimens at museums and in academic teaching collections. A full list of institutions can be found in the supplemental document for our paper.