Supporting data: Functional plasticity of the swim bladder as an acoustic organ for communication in a vocal fish
Data files
Dec 07, 2023 version files 10.25 MB
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background1.txt
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background10.txt
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background2.txt
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background3.txt
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background4.txt
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background5.txt
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background6.txt
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background7.txt
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background8.txt
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background9.txt
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displacementRMS.m
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ExtractData.m
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Fig1E-H.m
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Fig1i.m
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Fig2.m
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Fig3.m
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Fig4.m
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FigS1.m
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FigS2.m
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FigS5.m
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Nonreproductive.csv
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Nonreproductive130.csv
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Nonreproductive142.csv
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Nonreproductive154.csv
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NormalizedHornLength.csv
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NormalizedWidth.csv
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nr000.txt
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nr045.txt
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nr090.txt
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nr135.txt
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nr180.txt
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nr225.txt
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nr270.txt
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nr315.txt
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NRC-PN2201-r1.xls
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NRC-PN2201-r2.xls
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NRC-PN2205-r1.xls
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NRC-PN2205-r2.xls
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NRC-PN2206-r1.xls
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NRC-PN2206-r2.xls
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NRC-PN2207-r1.xls
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NRC-PN2207-r2.xls
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NRC-PN2208-r1.xls
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NRC-PN2208-r2.xls
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NRC-PN2209-r1.xls
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NRC-PN2209-r2.xls
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NRC-PN2216-r1.xls
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NRC-PN2216-r2.xls
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NRC-PN2218-r1.xls
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NRC-PN2218-r2.xls
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NRC-PN2219-r1.xls
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NRC-PN2219-r2.xls
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NRC-PN2222-r1.xls
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NRC-PN2222-r2.xls
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NRC-PN2223-r1.xls
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NRC-PN2223-r2.xls
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NRC-PN2224-r1.xls
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NRC-PN2224-r2.xls
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NRC.csv
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nrIO.csv
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nrNatFreq_grouped.csv
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nrNatFreq.csv
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NRR-PN2202-r1.xls
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NRR-PN2203-r1.xls
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NRR-PN2203-r2.xls
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NRR-PN2204-r1.xls
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NRR-PN2204-r2.xls
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NRR-PN2210-r1.xls
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NRR-PN2210-r2.xls
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NRR-PN2210-r3.xls
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NRR-PN2211-r1.xls
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NRR-PN2211-r2.xls
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NRR-PN2212-r1.xls
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NRR-PN2213-r1.xls
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NRR-PN2213-r2.xls
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NRR-PN2214-r1.xls
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NRR-PN2214-r2.xls
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NRR-PN2215-r1.xls
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NRR-PN2215-r2.xls
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NRR-PN2217-r1.xls
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NRR-PN2217-r2.xls
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NRR-PN2220-r1.xls
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NRR-PN2221-r1.xls
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NRR-PN2221-r2.xls
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NRR.csv
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pcScores.csv
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plotIsoIntensity2.m
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plotSPL.m
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plotTankAcoustics.m
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PM-095-130.txt
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PM-095-142.txt
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PM-095-154.txt
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PM-190-130.txt
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PM-190-142.txt
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PM-190-154.txt
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PM-285-130.txt
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PM-285-142.txt
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PM-285-154.txt
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PM-380-130.txt
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PM-380-142.txt
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PM-380-154.txt
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PM-475-130.txt
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PM-475-142.txt
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PM-475-154.txt
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PM-570-130.txt
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PM-570-142.txt
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PM-570-154.txt
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PM-665-130.txt
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PM-665-142.txt
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PM-665-154.txt
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PM-760-130.txt
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PM-760-142.txt
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PM-760-154.txt
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PM-855-130.txt
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PM-855-142.txt
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PM-855-154.txt
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PM-950-130.txt
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PM-950-142.txt
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PM-950-154.txt
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RC-PN2240-r1.xls
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RC-PN2240-r2.xls
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RC-PN2241-r1.xls
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RC-PN2241-r2.xls
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RC-PN2242-r1.xls
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RC-PN2242-r2.xls
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RC-PN2257-r1.xls
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RC-PN2257-r2.xls
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RC-PN2258-r1.xls
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RC-PN2258-r2.xls
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RC-PN2260-r1.xls
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RC-PN2261-r1.xls
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RC-PN2261-r2.xls
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RC-PN2262-r1.xls
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RC-PN2262-r2.xls
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RC-PN2263-r1.xls
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RC-PN2263-r2.xls
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RC-PN2264-r1.xls
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RC-PN2264-r2.xls
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RC-PN2265-r1.xls
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RC-PN2265-r2.xls
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RC-PN2265-r3.xls
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RC-PN2266-r1.xls
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RC-PN2266-r2.xls
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RC.csv
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README.md
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redblue.m
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rep000.txt
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rep045.txt
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rep090.txt
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rep135.txt
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rep180.txt
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rep225.txt
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rep270.txt
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rep315.txt
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repIO.csv
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repNatFreq_grouped.csv
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repNatFreq.csv
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Reproductive.csv
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Reproductive130.csv
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Reproductive142.csv
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Reproductive154.csv
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RR-PN2253-r1.xls
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RR-PN2253-r2.xls
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RR-PN2254-r1.xls
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RR-PN2254-r2.xls
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RR-PN2255-r1.xls
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RR-PN2255-r2.xls
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RR-PN2256-r1.xls
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RR-PN2256-r2.xls
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RR-PN2259-r1.xls
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RR-PN2259-r2.xls
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RR-PN2267-r1.xls
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RR-PN2267-r2.xls
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RR-PN2268-r1.xls
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RR-PN2269-r1.xls
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RR-PN2269-r2.xls
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RR-PN2270-r1.xls
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RR-PN2270-r2.xls
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RR-PN2271-r1.xls
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RR-PN2272-r1.xls
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RR-PN2273-r1.xls
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RR-PN2273-r2.xls
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RR-PN2274-r1.xls
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RR-PN2274-r2.xls
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RR.csv
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SB-to-OtolithDistance.csv
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Seasonal130.csv
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Seasonal142.csv
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Seasonal154.csv
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SeasonalThresholds.csv
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SMSI.csv
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Abstract
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.
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Author Information
A. Principle Investigator
Joseph A. Sisneros
University of Washington
Seattle, WA 98195
sisneros@uw.eduB. Corresponding Author
Loranzie S. Rogers
Harvard University
Cambridge, MA 02138
loranzierogers@fas.harvard.edu -
Date of data collection: February 2022 - July 2022
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Geographic location of data collection: Puget Sound and Hood Canal, WA, USA
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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
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Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
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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
- 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
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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).
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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.
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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).
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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).
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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.
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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.
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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.
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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.
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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.
Swim bladder morphometrics:
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.
Auditory sensitivity:
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.
Finite element analysis:
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/m3). 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 × 10-6 Newtons over a ~3.03 × 10-6 m2 area of elements, such that a global pressure load of 1 Pascal.
All data were anlyzed using custom MATLAB or R scripts.