The avian vocal system: 3D reconstruction reveals upper vocal tract elongation during head motion
Data files
Oct 24, 2024 version files 578.86 MB
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Extracted_from_XMALab.zip
561.51 MB
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Extracted_motion_data_from_Maya.zip
17.34 MB
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README.md
3.42 KB
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Rscripts.zip
5.38 KB
Abstract
While birds' impressive singing abilities are made possible by the syrinx, the upper vocal system (i.e., trachea, larynx, and beak) could also play a role in sound filtration. Yet, we still lack a clear understanding of the range of elongation this system can undertake, especially along the trachea. Here, we used biplanar cineradiography and X-ray Reconstruction of Moving Morphology (XROMM) to record 15 species of cadaveric birds from 9 different orders while an operator moved the bird’s cadaveric heads in different directions. In all studied species, we found elongation of the trachea to be correlated with neck extension, and significantly greater (ranging from 18% to 48% for the whole motion; and from 1.4% to 15.7% for the singing positions) than previously reported on a live singing bird (3%). This elongation or compression was not always homogeneous along its entire length. Some specimens showed increased lengthening in the rostral part and others in both the rostral and caudal parts of the vocal tract. The diversity of elongation patterns shows that trachea elongation is more complex than previously thought. Since tracheal lengthening affects sound frequencies, our results contribute to our understanding of the mechanisms involved in complex communication signals, one of the amazing traits we share with birds.
https://doi.org/10.5061/dryad.6t1g1jx7q
Description of the data and file structure
This Readme file was generated on 2024.10.04 by Fournier M.
Dataset: Data associated with the publication Fournier M., Olson R., Van Wassenbergh S. and Provini P. (2024). The avian vocal system: 3D reconstruction reveals upper vocal tract elongation during head motion. Journal of Experimental Biology.
General information
Principal Investigator: Morgane Fournier, Universitat Bern, mo.g.fournier@gmail;COM
Associate or Co-investigators: Rachel Olson, University of Akron, rolson@uakron.edu; Sam Van Wassenbergh, Universiteit Antwerpen, sam.vanwassenbergh@uantwerpen.be; Pauline Provini, Muséum National d’Histoire Naturelle, pauline.provini@mnhn.fr
Date of data collection (approximate date): 2021-2022
Geographic location of data collection: Anvers University, Belgium / Learning Planet Institute in Paris, France
Files and variables
File: Rscripts.zip
Description:
- Cor_tests: R scripts for correlation tests to be carried out on “4_Cor_tests” data.
- Motion_analyses: R scripts for figures.
File: Extracted_motion_data_from_Maya.zip
Description: files extracted from the 3D animation software (Maya) to study the movement of vocal tract locators (.csv).
- 0_Row_data: 3D coordinates of each vocal tract locator (10 generated locators from the glottis to the syrinx) during movement, for all frames.
- 1_Filtered_data: 3D coordinates of each vocal tract locator filtered, to remove artefacts and unrealistic movements, for each specimen.
- 2_for_frontal_view: 3D coordinates of each vocal tract locator for the selected position for front view graphics, for each specimen
- 3_for_lateral_view: 3D coordinates of each vocal tract locator for selected position for lateral view graphics, for each specimen.
- 4Cor_tests: files for the correlation tests. “Neck_extension&_trachea_elongation.ods” contains distance data representing the neck extension and length of the vocal tract during the movement for all the specimens. The file “for_larynx_cor_test” includes distances between the trachea and larynx markers; and distance between the trachea and glottis locator during the movement (a .csv file for each specimen).
File: Extracted_from_XMALab.zip
Description: Files extracted from the XMALab software to be imported into the 3D animation software to reconstruct the movement.
Inside the file for each specimen studied:
- Markers: 3D coordinates of each marker implanted during movement (.csv).
- RigidBodies: 3D coordinates of each rigid body (head and trunk) during movement (.csv) and the 3D object of these rigid bodies associated (.obj).
Code/software
Software:
- XMALab (version 2.0.1; Knörlein et al., 2016)
- Maya (version 2020.4; Autodesk)
Access information
Licenses/restrictions placed on the data, or limitations of reuse: CC0 public domain, without restriction on use
Recommended citation for the data: Fournier M., Olson R., Van Wassenbergh S. and Provini P. (2024). The avian vocal system: 3D reconstruction reveals upper vocal tract elongation during head motion. Dryad Digital Repository.