This readme.txt file was generated on 20221108 by Jackie Culotta Suggested citation: Culotta, Jackie; Vetter, Brooke, J; Mensinger, Allen, F; Kramer, Cassandra, A; Ervin, Marie, L. (2023). Chemotaxis and phonotaxis in a two-choice shuttle tank by bigheaded carps. Retrieved from the Data Repository for the University of Minnesota, https://hdl.handle.net/11299/252999. ------------------- GENERAL INFORMATION ------------------- 1. Data in support of "Acoustic and chemical conditioning and retention for behavioral deterrence in invasive bigheaded carps (Hypophthalmichthys molitrix and H. nobilis)" 2. Author Information Principal Investigator Contact Information Name: Allen Mensinger Institution: University of Minnesota Duluth Address: 1035 Kirby Drive, 13 Swenson Science Building, Duluth, MN 55812 Email: amensing@d.umn.edu Associate or Co-investigator Contact Information Name: Jackie Culotta Institution: University of Minnesota Duluth Email: culottajackie@gmail.com ORCID: 0000-0002-2533-0802 Name: Brooke Vetter Institution: University of Saint Thomas Email: brooke.vetter@stthomas.edu Name: Cassandra Kramer Institution: University of Saint Thomas Email: cassie@kramersonline.org Name: Marie Ervin Institution: University of Saint Thomas Email: marieervin00@gmail.com 3. Date published or finalized for release: 4/6/2023 4. Date of data collection (approximate range): 20210601 - 20220831 5. Geographic location of data collection (where was data collected?): MAISRC Containment Lab, 1995 Fitch Ave, Falcon Heights, MN 55108 6. Information about funding sources that supported the collection of the data: Funding for this project was provided by the Minnesota Environment and Natural Resources Trust Fund as recommended by the Minnesota Aquatic Invasive Species Research Center (MAISRC) and the Legislative-Citizen Commission on Minnesota Resources (LCCMR). 7. Overview of the data (abstract): Dissolved carbon dioxide avoidance in silver and bighead carps. Additionally, carp were conditioned to associate broadband sound from outboard boat motors (0.06 – 10 kHz, ~150 dB re 1 μPa) with CO2 application (~35,000 ppm). Phonotaxis trials were conducted over one to four weeks in a both a small (80 L) and large (3475 L) two-choice shuttle tank. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) https://creativecommons.org/licenses/by-nc/4.0/ 2. Links to publications that cite or use the data: 3. Was data derived from another source? No If yes, list source(s): 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: CO2_Avoidance.zip Short description: Contains files related to the CO2_Avoidance experiment CO2_Avoidance.Rmd: Calculates pCO2 avoidance thresholds in the small and large tank. CO2_Avoidance.pdf: Compiled version of RMD CO2_Map.R: Script to visualize pH/CO2 trends CO2_Map_Small.csv: Values for pCO2 in small tank CO2_Map_Large.csv: Values for pCO2 in large tank allFish_pH_CO2_curve.csv: Measured pH and pCO2 for all fish avoidance behaviors pH_to_CO2.R: Conversion of pH to pCO2 Exp1_SmallTank_CO2_Avoidance.csv: CO2 avoidance data in small tank Exp1_LargeTank_CO2_Avoidance.csv: CO2 avoidance data in large tank B. Filename: LargeTank.zip Short description: Contains files related to the LargeTank Experiment LargeTank.Rmd: Mixed ANOVAs for first return and exit in the large tank. Paired t-tests computed for tracking metrics. LargeTank.pdf: Compiled version of RMD loadLargeTank.R: Loads source data LargeTank_Ethovision.csv: Data on fish behavior from automated tacking software LargeTank_Phonotaxis.csv: Data on fish behavior compiled manually pwc_and_boxplot.R: Used in LargeTank.Rmd to compute pairwise comparisons and generate boxplots C. Filename: SmallTank.zip Short description: Contains files for the Small Tank experiment SmallTank.Rmd: Mixed ANOVAs for first return and exit in the small tank. SmallTank.pdf: Compiled PDF SmallTank_Phonotaxis.csv: Data on fish behavior in small experiment D. Soundmaps.zip Short description: Contains files for the soundmap experiment soundmap.m: Code to generate soundmap in large tank Sound Map - Large Tank.csv: SPL recordings for large tank at all depths Soundmap_Large_onBottom.xlsx: SPL in large tank during playback at bottom tank depth Soundmap_Large_onMiddle.xlsx: SPL in large tank during playback at middle tank depth Soundmap_Large_onTop.xlsx: SPL in large tank during playback at top tank depth soundmap_small.m: Code to generate soundmap in small tank Sound Map - Small Tank.csv: SPL recordings for small tank at all depths Soundmap_Small_onBottom.xlsx: SPL in small tank during playback at bottom tank depth Soundmap_Small_onTop.xlsx: SPL in small tank during playback at top tank depth 2. Relationship between files: Each of the three experiments are analyzed separately. Carbon dioxide avoidance thresholds, and behavioral response data from the small and large tank are separate. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: See article associated with this dataset. 2. Methods for processing the data: See Rmd files. 3. Instrument- or software-specific information needed to interpret the data: R & R studio. Soundmaps require MatLab & signal processing toolbox. 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: NA 6. Describe any quality-assurance procedures performed on the data: NA 7. People involved with sample collection, processing, analysis and/or submission: Jackie Culotta -------------------------- DATA-SPECIFIC INFORMATION -------------------------- 1. Missing data codes: NA Not applicable NR Not recorded 2. Variable List (Predictors) A. Name: VID_ID Description: Identifier for each video file. B. Name: Fish_ID or School_ID Description: Identifier for each fish or school of five fish. C. Name: Sound Description: Whether sound was playing (during the trial), or not playing (ambient conditions during acclimation period). Sound, Acclimation D. Name: Speaker Description: Whether the active speaker was placed in the right or left chamber. Right, Left E. Name: TrainedWith Description: Conditioning treatment assignment in the large tank. CO2, Air F. Name: Trained Description: Conditioning treatment assignment in the small tank. 0 days, 2 days G. Name: Days_Since_Train Description: The number of days since the fish or school underwent conditioning. H. Name: pH Description: Ambient water pH at trial onset, unless otherwise noted. I. Name: Temp_C Description: Ambient water temperature in celsius at trial onset. J. Name: Time Description: Approximate time of trial. Rounded to the nearest 15 minute mark. K. Name: Fish_TrialNum Description: The trial number for that fish or school of fish. L. Name: Species Description: Species of the experimental animal(s). Silver, Bighead M. Name: Stopped_Sound_On_Return Description: Whether sound was stopped after fish returned to speaker side or continued for trial duration. FALSE, TRUE N. Name: dB Description: Sound pressure level (SPL) in decibels. O. Name: RMS Description: Mean root mean square voltage to calculate SPL 3. Variable List (Response) A. Name: Exit_N Description: Number of shuttles away from the active speaker side. B. Name: Return_N Description: Number of shuttles towards the active speaker side. C. Name: Exit_s Description: Seconds until first shuttle away from the active speaker side. D. Name: Return_s Description: Seconds in opposite chamber until first shuttle towards the active speaker side. 4. Variable List (Other) TA_ppm: Water total alkalinity in parts per million pH: Water pH units ppm: CO2 in parts per million Seconds: Time since trial initiation in seconds Time: Time of day at trial initiation CO2_Stone: pH measurement at CO2 airstone CO2_Center: pH measurement at center of CO2 chamber CO2_Exit: pH measurement at exit of CO2 chamber Air_Exit: pH measurement at ambient airstone Air_Center: pH measurement at center of air chamber Air_Stone: pH measurement at air chamber exit ID: trial ID Date: date of trial School: School of fish ID Species: Species of fish CO2_Side: Side of tank that received CO2 input Alkalinity_ppm: Water total alkalinity in parts per million Initial_pH: Water pH before trial initiation X1st_Avoid_pH: pH when fish first left CO2 chamber X1st_Avoid_Measured_CO2_ppm: Measured pCO2 when fish left CO2 chamber Last_Avoid_pH: pH when fish last left CO2 chamber Last_Avoid_Estimated_CO2_ppm: Estimated pCO2 when fish left CO2 chamber in ppm End_Trial_Measured_CO2_ppm: Measured pCO2 at end of tiral Last_Avoid_Calc_CO2_uatm: Estimated pCO2 when fish left CO2 chamber in microatmospheres X1st_LOE_pH: pH at loss of equilibrium, if applicable Fish1_cm: Total length of fish 1 in cm Fish2_cm: Total length of fish 2 in cm Fish3_cm: Total length of fish 3 in cm Fish4_cm: Total length of fish 4 in cm Fish5_cm: Total length of fish 5 in cm Notes: Qualitative notes on trial run VID_ID: Video recording identification number CO2_Output_uAtm: Estimated pCO2 in microatmospheres measured_pCO2_ppm: Measured pCO2 in parts per million Avoid_pH_Input: pH value Alkalinity_Pre: Water total alkalinity in parts per million before trial Day: Day since conditioning (factor) Fish_ID: Fish identificiation number Sound: Sound or ambient conditions Speaker: Right or left speaker chosen for playback TrainedWith: Conditioning treatment with air or CO2 DistanceMoved_cm: Total fish distance moved Velocity: Average fish velocity over trial RightDistance_cm: Average distance from right speaker LeftDistance_cm: Average distance from left speaker NotMoving_per: Percentage of time not moving Accel_mean: Mean fish acceleration Accel_max: Max fish acceleration Accel_sd: Standard deviation of acceleration TimeToRight_s: Time in seconds to move to the right side InRight_per: Percentage of trial time in right chamber TimeToLeft_s : Time in seconds to move to the left side InLeft_per: Percentage of trial time in left chamber HeadingToLeft_deg: Degrees of heading between fish orientation and left speaker at onset HeadingToRight_deg: Degrees of heading between fish orientation and right speaker at onset Days_Since_Train: Days since conditioning (numerical) Fish_TrialNum: The count of trials experienced by a fish or school Stopped_Sound_On_Return: Whether playback was stopped on fish return loud chamber Frequency_Hz: Frequency of sound used (puretones, Hz vs. BB for broadband) Angle: Angle of fish to exit dB_65_cm: SPL in dB at 65 cm depth RMS_65_cm: Root mean square of voltage recorded at 65 cm depth X_cm: X coordinate in cm Y_cm: Y coordinate in cm Circle: Concentric circle within tank Side: Right or left side of tank Position: Recording position number in tank Depth: Recording depth Ambient: Ambient conditions or during playback PA: Particle acceleration value X_acc_ms..2: Calculation of PA in X plane Y_acc_ms..2: Calculation of PA in Y plane Z_acc_ms..2: Calculation of PA in Z plane X_RMS_V: Root mean square of voltage in X plane Y_RMS_V: Root mean square of voltage in Y plane Z_RMS_V: Root mean square of voltage in Z plane dB: SPL in dB dB_2: SPL in dB on backup measurement RMS: Root mean square of voltage for SPL RMS_2: Root mean square of voltage for SPL on backup measurement ----------------------- R Session Information ----------------------- locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils [5] datasets methods base other attached packages: [1] gdata_2.18.0.1 lme4_1.1-30 Matrix_1.5-1 [4] rstatix_0.7.0 stringr_1.4.1 reshape2_1.4.4 [7] ggpubr_0.4.0 ggplot2_3.3.6 dplyr_1.0.10 loaded via a namespace (and not attached): [1] gtools_3.9.3 tidyselect_1.1.2 [3] xfun_0.33 purrr_0.3.4 [5] splines_4.1.0 lattice_0.20-44 [7] carData_3.0-5 colorspace_2.0-3 [9] vctrs_0.4.1 generics_0.1.3 [11] htmltools_0.5.3 yaml_2.3.5 [13] utf8_1.2.2 rlang_1.0.5 [15] nloptr_2.0.3 pillar_1.8.1 [17] glue_1.6.2 withr_2.5.0 [19] DBI_1.1.3 lifecycle_1.0.2 [21] plyr_1.8.7 munsell_0.5.0 [23] ggsignif_0.6.3 gtable_0.3.1 [25] evaluate_0.16 labeling_0.4.2 [27] knitr_1.40 fastmap_1.1.0 [29] fansi_1.0.3 broom_1.0.1 [31] Rcpp_1.0.9 backports_1.4.1 [33] scales_1.2.1 abind_1.4-5 [35] farver_2.1.1 digest_0.6.29 [37] stringi_1.7.6 grid_4.1.0 [39] cli_3.4.0 tools_4.1.0 [41] magrittr_2.0.3 tibble_3.1.8 [43] tidyr_1.2.1 car_3.1-0 [45] pkgconfig_2.0.3 ellipsis_0.3.2 [47] MASS_7.3-54 assertthat_0.2.1 [49] minqa_1.2.4 rmarkdown_2.16 [51] rstudioapi_0.14 R6_2.5.1 [53] boot_1.3-28 nlme_3.1-152 [55] compiler_4.1.0