DOI: 10.5061/dryad.msbcc2g1k
title: Realistic 3D avian vocal tract model demonstrates how shape affects sound filtering (Passer domesticus)

description: Despite the complex geometry of songbird’s vocal system, it was typically
 modelled as a tube or with simple mathematical parameters to investigate
 sound filtering. Here, we developed an adjustable computational acoustic
 model of a sparrow’s upper vocal tract (Passer domesticus), derived from
 micro-CT scans. We discovered that a 20% tracheal shortening or a 20° beak
 gape increase caused the vocal tract harmonic resonance to shift towards
 higher pitch (11.7% or 8.8%, respectively), predominantly in the mid-range
 frequencies (3-6 kHz). The oropharyngeal-esophageal cavity (OEC), known
 for its role in sound filtering, was modelled as an adjustable 3D
 cylinder. For a constant OEC volume, an elongated cylinder induced a
 higher frequency shift than a wide cylinder (70% versus 37%). We found
 that the OEC volume adjustments can modify the OEC first harmonic
 resonance at low frequencies (1.5–3 kHz) and the OEC third harmonic
 resonance at higher frequencies (6-8 kHz). This work demonstrates the need
 to consider the realistic geometry of the vocal system to accurately
 quantify its effect on sound filtering and show that sparrows can tune the
 entire range of produced sound frequencies to their vocal system
 resonances, by controlling the vocal tract shape, especially through
 complex OEC volume adjustments.
description: The dimensions of the trachea,
 larynx, beak, tongue, and other anatomical features derive from CT scan
 images of a whole-body specimen of a house sparrow, preserved in 70%
 ethanol and stained with iodine-potassium iodine dissolved in water for
 four weeks (Morphosource: usnm:birds:657964 Passer domesticus –
 ark:/87602/m4/M115379). The device used to acquire these images was a
 General Electric phoenix v|tome|x m, Smithsonian Institution Bio-Imaging
 Research (SIBIR) Center (National Museum of Natural History, Smithsonian
 Institution), with a X, Y, and Z pixel spacing of 0.067805 mm. The
 contrast agent used to prepare the specimen allows for the visualisation
 of soft tissues (tongue, cheeks, etc.) and provides accurate modelling of
 the entire 3D vocal system shape, in place. This specimen was used to
 investigate the chemical effects of staining (Early et al., 2020),
 therefore it corresponds to a well-preserved specimen, prepared in optimal
 condition for CT-scan acquisition. Bone demineralization occurs throughout
 the staining process (Early et al., 2020), but we chose a CT-scan
 performed after 4 weeks of staining, which minimize the risk of tissue
 degradation, while providing a satisfactory 3D model quality. We segmented
 the CT scan, using Avizo (v. 9.7, FEI Visualisation Sciences Group,
 Burlington, MA, USA). We extracted the upper beak, lower beak, tongue, and
 rest of the body, as separate 3D objects. To save solver time without
 losing any accuracy, we reduced the 3D object to the upper body only, and
 smoothed the external body, while preserving the entire trachea and the
 rest of the upper vocal tract. We imported the 3D objects into COMSOL
 (COMSOL,
 2021) Multiphysics®
 software to build the initial model, which we digitally modified to test
 the influence of each structure on sound modulation (Figure 1A). The initial model has a 30.58 mm long
 trachea and a 10-degree beak gape with the larynx’ opening, the glottis,
 around 0.7 mm in radius. Trachea
 To assess the effect of
 trachea shortening, we cut 7%, 11%, and 20% of the initial model trachea
 (Figure
 1B, respectively). We
 modelled extreme elongation or shortening to test the potential effect of
 trachea lengthening, our personal observations on cadavers led us to test
 a maximum of 20% variation. We used the “differences” tool in COMSOL
 Multiphysics® software (COMSOL, 2021). We considered the end correction and added a
 short distance to the actual length of the beak (Bosanquet, 1878; Levine and Schwinger,
 1948). Glottis
 We started with a 0.5 mm
 glottis diameter, corresponding to the geometry of the µCT scan. For that,
 we inserted a cylinder in the original larynx and cut the cylinder surface
 area to decrease the diameter of the glottis. It resulted in a sharp edge
 at the junction of the glottis and the cylinder. We compared the result for a geometry with a
 smooth surface or a sharp edge. The difference was inferior to 1%.
 Therefore, we considered that the effect was negligeable.
 With this method, we
 decreased the radius by 0.1 mm steps to reach a final radius of 0.1 mm
 (Figure
 1C). Tongue As the tongue was previously segmented, we were
 able to move it in COMSOL Multiphysics® software, using the rotation tool
 (COMSOL,
 2021). We considered the
 tongue in 3 different positions: 1) the tongue touches the lower beak, 2)
 the tongue is located in the middle of the beaks, and 3) the tongue
 touches the upper beak. We chose these conformations to mimic the
 potential motions of the tongue during vocalisation, from the lower to the
 upper beak. We compared those three models with the initial model without
 tongue (Figure
 1D). Beak opening
 We imported the beak 3D models
 derived from the segmentation, in Autodesk Maya (Student version 2020). We
 placed a virtual joint at the approximate location of the lower beak joint
 (Baumel,
 1993)
 (Figure
 1E). We chose three beak poses, representing
 extreme beak gape angles: 10°, 20°, and 30°. 
 OEC
 Based on the location and
 shape of the oropharyngeal cavity (OEC) on the µCT-scan data, we
 artificially added a curved cylindric shape of 0.4 mL to the initial model
 (Figure 6). To investigate the role of the 3D shape on sound modulation,
 we modelled the OEC in seven different volumes (1.4, 1.3, 1.2, 1.1, 1,
 0.9, and 0.8 mL) (Figure
 4), by adding a cylindric
 shape to the initial curved cylinder and by incrementally changing its
 length: 8, 10, 12, 14, 16, 18, and 20 mm (Figure 6A), and radius: 2.5 , 2.8 , 3.1 , 3.34 , 3.57 ,
 3.78 , 4 mm (Figure
 6B). We estimated the
 volume of the OEC using previous X-ray video recordings of OEC movements
 during vocalisation (Fletcher et al., 2006; Riede and Suthers, 2009;
 Riede et al., 2006). We
 checked the effect of the connection between the cylinder and torus, and
 between the torus and the buccal cavity in each model. The effect was
 inferior to 1%, thus considered ignorable.
description: You need COMSOL Multiphysics® (COMSOL, 2021) software to open the
 models.