DOI: 10.5061/dryad.ffbg79d1t
title: Supporting data: Functional plasticity of the swim bladder as an acoustic organ for communication in a vocal fish

description: In this study, we show that the swim bladder of male plainfin midshipman
 fish (Porichthys notatus) exhibits reproductive state-dependent changes in
 morphology and function for sound production and reception. We quantified
 swim bladder morphometrics and utilized psuedolandmarking to identify
 differences in nonreproductive and reproductive male swim bladders. We
 utilized auditory evoked potential recordings, to measure the auditory
 sensitivity of saccular hair cells in response to sound pressure levels
 ranging from 97 - 154 dB re: 1 µPa to determine how the swim bladder
 contributes to midshipman auditory sensitivity. Finally, we used finite
 element modeling to explore the frequency response of nonreproductive and
 reproductive male swim bladders.
description: <em>Swim bladder morphometrics: </em>
 Nonreproductive and reproductive male plainfin midshipman were CT
 scanned and reconstructed using Slicer software. Following recontruction,
 swim bladder width, length, and horn length were calculated. Swim bladders
 were then pseudo-landmarked and compared using PCA analysis.
 <em>Auditory sensitivity: </em>
 Auditory evoked potentials were recorded from saccular hair cells
 in nonreproductive and reproductive male midshipman with swim bladders
 that were intact (i.e., control) or ablated (i.e., removed) using glass
 microelectrodes. Evoked potentials were recorded in response to pure tone
 stimuli (95 - 950 Hz) at sound pressure levels ranging from 97 - 154 dB
 re: 1 µPa. All experiments were performed in MATLAB.
 <em>Finite element analysis:</em>
 Models of nonreproductive and reproductive male swim bladders
 from 3D Slicer were imported into FreeCad and sectioned into 22.5 degree
 increments before  being exported to Strand7. Models were then meshed with
 triangular elements and given material properties (1 MPa), thickness
 (824.5 mm) and density (1000 kg/m<sup>3</sup>). For dynamic
 analysis, swim bladders were considered to be underdamped with a damping
 ratio of 0.325. Then natural frequencies, displacement, and power were
 determined in Strand7. Measurements were determined in response to a total
 force of 3.03 × 10<sup>-6</sup> Newtons over a ~3.03 ×
 10<sup>-6</sup> m<sup>2</sup> area of elements,
 such that a global pressure load of 1 Pascal. All data
 were anlyzed using custom MATLAB or R scripts.
description: # 'Supporting data: Functional plasticity of the swim bladder as an
 acoustic organ for communication in a vocal fish' 1. Author
 Information A. Principle Investigator Joseph A. Sisneros University of
 Washington Seattle, WA 98195 B. Corresponding
 Author Loranzie S. Rogers Harvard University Cambridge, MA 02138
 2. Date of data collection:
 February 2022 - July 2022 3. Geographic location of data collection: Puget
 Sound and Hood Canal, WA, USA 4. Funding Sources NSF-IOS-1933166 (J.A.S)
 Lerner-Gray Memorial Fund of the American Museum of Natural History
 (N.R.L.) NIH T32DC005361 (N.R.L.) Bloedel Hearing fellowship (J.L.D.)
 Fulbright fellowship and No. 0279-2021-0005 (121032300224-8) (Y.P.S.)
 Howard Hughes Medical Institute Gilliam Fellowship grant no. GT15044
 (L.S.R.) SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the
 data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Recommended citation
 for this dataset: Rogers LS, Lozier NR, Sapozhnikova YP, Diamond KA, Davis
 JL, and Sisneros JA (2023). Supporting Data: Functional plasticity of the
 swim bladder as an acoustic organ in a vocal fish. Dryad Digital
 Repository. DOI: 10.5061/dryad.ffbg79d1t DATA & FILE OVERVIEW 1. File
 List: A. Data analysis Nonreproductive.csv Nonreproductive130.csv
 Nonreproductive142.csv Nonreproductive154.csv Reproductive.csv
 Reproductive130.csv Reproductive142.csv Reproductive154.csv
 Seasonal130.csv Seasonal142.csv Seasonal154.csv SeasonalThresholds.csv B.
 Figure 1 Fig1E-H.m Fig1i.m NormalizedHornLength.csv NormalizedWidth.csv
 pcScores.csv SB-to-OtolithDistance.csv SMSI.csv C. Figure 2 Fig2.m NRC.csv
 plotIsoIntensity2.m plotSPL.m RC.csv D. Figure 3 Fig3.m NRC.csv NRR.csv
 plotSPL.m RC.csv RR.csv E. Figure 4 displacementRMS.m ExtractData.m Fig4.m
 nr000.txt nr045.txt nr090.txt nr135.txt nr180.txt nr225.txt nr270.txt
 nr315.txt nrNatFreq_grouped.csv nrNatFreq.csv redblue.m rep000.txt
 rep045.txt rep090.txt rep135.txt rep180.txt rep225.txt rep270.txt
 rep315.txt repNatFreq_grouped.csv repNatFreq.csv F. Figure S1 FigS1.m
 nrIO.csv repIO.csv G. Figure S2 background1.txt background2.txt
 background3.txt background4.txt background5.txt background6.txt
 background7.txt background8.txt background9.txt background10.txt FigS2.m
 plotTankAcoustics.m PM-095-130.txt PM-095-142.txt PM-095-154.txt
 PM-190-130.txt PM-190-142.txt PM-190-154.txt PM-285-130.txt PM-285-142.txt
 PM-285-154.txt PM-380-130.txt PM-380-142.txt PM-380-154.txt PM-475-130.txt
 PM-475-142.txt PM-475-154.txt PM-570-130.txt PM-570-142.txt PM-570-154.txt
 PM-665-130.txt PM-665-142.txt PM-665-154.txt PM-760-130.txt PM-760-142.txt
 PM-760-154.txt PM-855-130.txt PM-855-142.txt PM-855-154.txt PM-950-130.txt
 PM-950-142.txt PM-950-154.txt H. Figure S5 FigS5.m I. Threshold Files
 NRC-PN2201-r1.xls NRC-PN2201-r2.xls NRC-PN2205-r1.xls NRC-PN2205-r2.xls
 NRC-PN2206-r1.xls NRC-PN2206-r2.xls NRC-PN2207-r1.xls NRC-PN2207-r2.xls
 NRC-PN2208-r1.xls NRC-PN2208-r2.xls NRC-PN2209-r1.xls NRC-PN2209-r2.xls
 NRC-PN2216-r1.xls NRC-PN2216-r2.xls NRC-PN2218-r1.xls NRC-PN2218-r2.xls
 NRC-PN2219-r1.xls NRC-PN2219-r2.xls NRC-PN2222-r1.xls NRC-PN2222-r2.xls
 NRC-PN2223-r1.xls NRC-PN2223-r2.xls NRC-PN2224-r1.xls NRR-PN2202-r1.xls
 NRR-PN2203-r1.xls NRR-PN2203-r2.xls NRR-PN2204-r1.xls NRR-PN2204-r2.xls
 NRR-PN2210-r1.xls NRR-PN2210-r2.xls NRR-PN2210-r3.xls NRR-PN2211-r1.xls
 NRR-PN2211-r2.xls NRR-PN2212-r1.xls NRR-PN2212-r2.xls NRR-PN2213-r1.xls
 NRR-PN2213-r2.xls NRR-PN2214-r1.xls NRR-PN2214-r2.xls NRR-PN2215-r1.xls
 NRR-PN2215-r2.xls NRR-PN2217-r1.xls NRR-PN2217-r2.xls NRR-PN2220-r1.xls
 NRR-PN2220-r2.xls NRR-PN2221-r1.xls NRR-PN2221-r2.xls RC-PN2240-r1.xls
 RC-PN2240-r2.xls RC-PN2241-r1.xls RC-PN2241-r2.xls RC-PN2242-r1.xls
 RC-PN2242-r2.xls RC-PN2257-r1.xls RC-PN2257-r2.xls RC-PN2258-r1.xls
 RC-PN2258-r2.xls RC-PN2260-r1.xls RC-PN2261-r1.xls RC-PN2261-r2.xls
 RC-PN2262-r1.xls RC-PN2262-r2.xls RC-PN2263-r1.xls RC-PN2263-r2.xls
 RC-PN2264-r1.xls RC-PN2264-r2.xls RC-PN2265-r1.xls RC-PN2265-r2.xls
 RC-PN2265-r3.xls RC-PN2266-r1.xls RC-PN2266-r2.xls RR-PN2253-r1.xls
 RR-PN2253-r2.xls RR-PN2254-r1.xls RR-PN2254-r2.xls RR-PN2255-r1.xls
 RR-PN2255-r2.xls RR-PN2256-r1.xls RR-PN2256-r2.xls RR-PN2259-r1.xls
 RR-PN2259-r2.xls RR-PN2267-r1.xls RR-PN2267-r2.xls RR-PN2268-r1.xls
 RR-PN2269-r1.xls RR-PN2269-r2.xls RR-PN2270-r1.xls RR-PN2270-r2.xls
 RR-PN2271-r1.xls RR-PN2272-r1.xls RR-PN2272-r2.xls RR-PN2273-r1.xls
 RR-PN2273-r2.xls RR-PN2274-r1.xls RR-PN2274-r2.xls
 \################################################################################################### DATA-SPECIFIC INFORMATION FOR: Data analysis files Nonreproductive.csv and Reproductive.csv: Files contain the auditory thresholds of nonreproductive and reproductive control (NRC and RC) and removal (NRR and RR) animals tested. Each row represents a unique fish at a give frequency (column). SeasonalThresholds.csv: Files contain the auditory thresholds on nonreproductive and reproductive control (NR and R) animals tested. Each row represents a unique fish at a give frequency (column). Nonreproductive130.csv, Nonreproductive142.csv, Nonreproductive154.csv, Reproductive130.csv, Reproductive142.csv, Reproductive154.csv, Seasonal130.csv, Seasonal142.csv, Seasonal154.csv: Files contain the evoked potential magnitudes (uV) of nonreproductive (NR) and reproductive (R) control (NRC and RC) and removal (NRR and RR) animals tested. Each row represents a unique fish at a given the give sound pressure level indicated (i.e., 130, 142, and 154 dB re: 1 u Pa). \################################################################################################### DATA-SPECIFIC INFORMATION FOR: Figure 1 files Fig1E-H.m and Fig1i.m: Matlab files that will recreate data plotted in figure 1e - i. Place all Figure 1 files indicated in the same location and press run. SMSI.csv: Sonic muscle somatic index from nonreproductive (nr) and reproductive (rep) male swim bladders in figure 1e. NormalizedWidth.csv: Normalized width of nonreproductive (nr) and reproductive (rep) male swim bladders in figure 1f. NormalizedHornLength.csv: Normalized length of nonreproductive (nr) and reproductive (rep) male swim bladders in figure 1g. SB-to-OtolithDistance.csv: Normalized distance between the rostral swim bladder and caudal saccular otolith of nonreproductive (nr) and reproductive (rep) male swim bladders in figure 1h. pcScores.csv: First two principle component scores of pseudo-landmarked nonreproductive (nr) and reproductive (rep) male swim bladders in figure 1h. \################################################################################################### DATA-SPECIFIC INFORMATION FOR: Figure 2 files Fig2.m: Matlab file for plotting figure 2 d-g. This requires that data listed under Threshold Files plotIsoIntensity2.m: matlab function required for Fig2.m to plot figure 2d. plotSPL.m: Matlab function required to plot figure 2e. NRC.csv and RC.csv: Files contain the auditory thresholds of nonreproductive (NRC) and reproductive (RC) control animals. Each row represents a unique fish at a give frequency (column). \################################################################################################### DATA-SPECIFIC INFORMATION FOR: Figure 3 files Fig3.m: Matlab file for plotting figure 3. plotSPL.m: Matlab function required to plot figure 3a and 3d. NRC.csv, NRR.csv, RC.csv, and RR.csv: Files contain the auditory thresholds of nonreproductive (NR) and reproductive (R) control (NRC and RC) and removal (NRR and RR) animals. Each row represents a unique fish at a give frequency (column). \################################################################################################### DATA-SPECIFIC INFORMATION FOR: Figure 4 files Fig4.m, displacementRMS.m, ExtractData.m, and redblue.m: Matlab files used to produce Figure 4. nr000.txt, nr045.txt, nr090.txt, nr135.txt, nr180.txt, nr225.txt, nr270.txt, nr315.txt: Nonrepreoductive swim bladder displacement values when impinging sound pressures were applied at various angles (0 - 315 deg in 45 degs) nrNatFreq_grouped.csv: number of natural frequencies grouped every 50 Hz for nonreproductive swim bladder. nrNatFreq.csv: Natural frequencies of nonreproductive swim bladder. rep000.txt, rep045.txt, rep090.txt, rep135.txt, rep180.txt, rep225.txt, rep270.txt, rep315.txt: Repreoductive swim bladder displacement values when impinging sound pressures were applied at various angles (0 - 315 deg in 45 degs) repNatFreq_grouped.csv: number of natural frequencies grouped every 50 Hz for reproductive swim bladder. repNatFreq.csv: Natural frequencies of reproductive swim bladder. \################################################################################################### DATA-SPECIFIC INFORMATION FOR: Figure S1 FigS1.m: Matlab code to plot data shown in figure S1. nrIO.csv and repIO.csv: Representative evoked potential responses at three representative frequencies (rows) across a range of sound pressure levels (columns) for nonreproductive (nr) and reproductive (rep) midshipman. \################################################################################################### DATA-SPECIFIC INFORMATION FOR: Figure S2 FigS2.m and plotTankAcoustics.m: Matlab files to produce data shown in Figure S2 background1.txt, background2.txt, background3.txt, background4.txt, background5.txt, background6.txt, background7.txt, background8.txt, background9.txt, background10.txt: Files containing background sound pressure levels recorded in the experimental tank. PM-095-130.txt, PM-095-142.txt, PM-095-154.txt, PM-190-130.txt, PM-190-142.txt, PM-190-154.txt, PM-285-130.txt, PM-285-142.txt, PM-285-154.txt, PM-380-130.txt, PM-380-142.txt, PM-380-154.txt, PM-475-130.txt, PM-475-142.txt, PM-475-154.txt, PM-570-130.txt, PM-570-142.txt, PM-570-154.txt, PM-665-130.txt, PM-665-142.txt, PM-665-154.txt, PM-760-130.txt, PM-760-142.txt, PM-760-154.txt, PM-855-130.txt, PM-855-142.txt, PM-855-154.txt, PM-950-130.txt, PM-950-142.txt, PM-950-154.txt: Data adhere to the following naming convention: PM-f0-dB; PM = particle motion; f0 is freq as three digits; dB = sound pressure (dB re: 1 uPa). Reference the matlab file 'FigS2.m' to see what each data column represents. \################################################################################################## DATA-SPECIFIC INFORMATION FOR: Figure S5 FigS5: Matlab code to generate data shown in Figure S5. Requires that all files under 'Threshold Files' are contained within the same working directory as the code. \################################################################################################### DATA-SPECIFIC INFORMATION FOR: Threshold Files Each file contains evoked potential data for nonreproductive control (NRC), nonreproductive removal (NRR), reproductive control (RC), and reproductive removal (RR). 'PNXXXX' indicates unique identifier for each fish tested. 'rX' represents recording number a given fish. Each row represents a given frequency (Hz) while each column represents a tested sound pressure level (dB re: 1 uPa). Each data file also has the 8 repeated responses and average evoke potential response at 130, 142, and 154 dB re: 1 uPa. ADDITIONAL NOTES For all files, NaN represents values that were either not recorded or not represented. In matlab these will be ignored using 'omitnan'. Any additional cells that are left blank are intentional and will be ignored in the custom scripts.