DOI: 10.5061/dryad.qz612jmqc
title: Data from: Intraspecific variation in metabolic responses of a cool water fish to increasing temperatures

description: Growing impacts of climate change necessitate predicting species'
 vulnerability to altered ecosystems. Assessing vulnerability requires
 understanding how species' physiology, life history, and ecology vary
 among populations and can be altered by behavioral, plastic, and
 evolutionary adaptations. To examine intraspecific variation in
 sensitivity to climate change, we measured metabolic responses to acute
 and chronic temperature exposures in three rearing pond populations of
 walleye (Sander vitreus), a cool-water-adapted fish species threatened by
 climate change. We show significant differences among rearing pond
 populations in response to increasing temperatures which may originate
 from broodstock, developmental plasticity, and acclimation. Our results
 indicate northern walleye may be more tolerant of acute and chronic
 exposure to higher temperatures by being able to maintain a higher aerobic
 scope than more southern populations. Furthermore, even over small
 geographic distances, populations can have significantly different
 physiological responses to environmental stressors. Quantifying variation
 in population-specific metabolic responses can inform predictions of
 growth, reproduction, and fitness across a species range and clarify the
 importance of within-species diversity in determining vulnerability to
 environmental stressors.
description: Metabolic rates were collected from walleye (<em>Sander
 vitreus</em>) using intermittent respirometry utilizing AutoResp
 v2.3.0 (Loligo Systems, Viborg, Denmark). Raw data was then processed
 using the FishResp package v.1.0.3 (Morozov et al. 2019) in R-Studio to
 calculate the standard metabolic rate, maximum metabolic rate, and
 absolute aerobic scope. Standard metabolic rate was calculated as the
 average of the lowest 20th percentile of measurements conducted over 16
 hours. Maximum metabolic rate was determined to be the highest rate
 observed across all respiration measurements through a chase routine.
 Aerobic scope was calculated as the absolute aerobic scope, meaning
 maximum metabolic rate minus standard metabolic rate. After these
 calculations metabolic rates were then analyzed following the R-script
 provided. Additional details pertaining to the methods used for subsequent
 analysis can be found in the published mansucript.
description: # Intraspecific variation in metabolic responses of a cool water fish to
 increasing temperatures
 [https://doi.org/10.5061/dryad.qz612jmqc](https://doi.org/10.5061/dryad.qz612jmqc) This repository contains the data and code that supports the manuscript: "Intraspecific Variation in Metabolic Responses of a Cool Water Fish to Increasing Temperatures" by Jackson S.A., Lucas K.N, Wehrly K.F., and Alofs K.M. Briefly, this manuscript investigates the role of intraspecific variation in response to increasing temperatures among several rearing pond populations of Walleye (Sander vitreus). Data contained within this repository were collected from Age-0 fish using intermittent respirometry. Raw data was then processed entirely in R using the R Package FishResp. The data used in the manuscript is located in the `Metabolism.Data.csv` file were then subsequently analyzed utilizing R for the analysis presented in the manuscript.  **Intraspecific_Variation_Walleye_Respirometry.zip -** Zipped project folder containing data and code used for analysis. The folder is structured as a GitHub Repository which can be found at [https://github.com/sajacks/Intraspecific-Variation-in-Metabolic-Responses-of-a-Cool-Water-Fish-to-Increasing-Temperatures](https://github.com/sajacks/Intraspecific-Variation-in-Metabolic-Responses-of-a-Cool-Water-Fish-to-Increasing-Temperatures)  Within the zip file the following folders and files can be found: **`Metabolism.Data.csv`** - Final dataset after data processing used for analysis in manuscript.   All analysis and figures were conducted in R-Studio using the `Metabolism.Analysis.R`file. Contents of **`Metabolism.Analysis.csv`** files * `FishIDs` = Numerical count of fish * `Stock` = Which genetic population fish came from, either LP, Lower Peninsula, or UP, Upper Peninsula * `Pond` = Which rearing pond fish came from, BC - Bay City, DB, Dearborn, ME, Menominee * `Trial `= Acute, or Acclimated, the two different experimental approaches to temperature exposure used in the experiments, acute - short-term, acclimated - long-term * `Chamber.No` = Which chamber 1-8 in the respirometry system fish were in during experiment * `Ind` = Unique identifier for fish, numerical * `Mass` = Wet mass (g) * `Volume` = Volume of respirometry chamber (mL) * `SMR.Start.Date` = start date and time of experiment, yyyy-mon-dd, hh:mm:ss * `SMR.Phase `= The type of phase and an ordinal number of measurement * `SMR.Temp.true` = Real time temperature during experiment (C) * `Temp.factor` = Factorial representation of temperature (C) * `Slope.with.BR.SMR` = Decline in oxygen due to fish respiration and background respiration (mg02/L/s) * `Slope.SMR`= Decline in oxygen due to just fish respiration (mg02/L/s) * `SE.SMR`= Standard error of SMR (mg02/L/s) * `R2.SMR`= R2 used for calculating metabolic rate from oxygen decline slopes * `MR.abs.with.BR` = Metabolic rate including background respiration (mg02/h) * `BR.SMR` = Background respiration during SMR (mg02/h) * `SMR.abs` = Standard metabolic rate, non-mass specific (mg02/min) * `SMR` = Standard metabolic rate, mass specific (mg02/h/kg) * `SMR.units`= Standard Metabolic rate, non-mass specific (mg02/min/kg) * `DO.unit` = DO concentration measurement unit * `MMR.Date` = mm/dd/yyyy * `MMR.Date.Time`= Start date and time of experiment, yyyy-mon-dd, hh:mm:ss * `MMR.Phase`= The type of phase and an ordinal number of measurement * `MMR.Temp.true` = Real time temperature during experiment (C) * `Slope.with.BR.MMR` = Decline in oxygen due to fish respiration and background respiration (mg02/L/s) * `Slope.MMR `= Decline in oxygen due to just  fish respiration (mg02/L/s) * `SE.MMR` = Standard error of MMR (mg02/L/s) * `R2.MMR` = R2 used for calculating metabolic rate from oxygen decline slopes * `MR.abs.with.BR.MMR `= Metabolic rate including background respiration (mg02/h) * `BR.MMR `= Background respiration during SMR (mg02/h) * `MMR.abs `= Maximum metabolic rate, non-mass specific (mg02/min) * `MMR `= Maximum metabolic rate, mass specific (mg02/h/kg) * `MMR.units` = Maximum metabolic rate, mass specific (mg02/min/kg) * `MMR.Best.Temp` = Temperature at which highest overall MMR was achieved (C) * `MMR.Best.abs.with.BR `= Metabolic rate including background respiration (mg02/h) * `MMR.Best.BR` = Metabolic rate (mg02/h) * `MR.Best.abs.MMR` =  Maximum metabolic rate, non-mass specific (mg02/min) * `MMR.Best `= Highest overall MMR from both SMR and MMR trials, (mg02/hr/kg) * `MMR.Best.units` = Highest overall MMR from both SMR and MMR trials units adjusted to minutes, (mg02/min/kg) * `Trial.Best.MMR` = Which trial did highest MMR occur in, SMR or MMR * `Experiment` = Numerical count of experiment  * `Replicate` = 1 - non repeated temperature during experiment, 2 - repeated temperature in experiment * `AS.absolute`= Absolute aerobic scope (MMR-SMR) calculated from subtracting SMR from highest MMR from just MMR trial, mgO2/min * `AS.absolute.units` = Mass specific absolute aerobic scope (MMR-SMR) calculated from subtracting SMR from highest MMR from just MMR trial adjusted from hours to minutes (mgO2/min) * `AS.factorial` = Factorial calculation of aerobic scope (MMR/SMR) using highest MMR from only MMR trial, unitless * `AS.Best.absolute` = Absolute aerobic scope (MMR-SMR) calculated from subtracting SMR from highest MMR (mgO2/h) * `AS.Best.factorial `= Factorial calculation of aerobic scope (MMR/SMR) using highest MMR from both MMR and SMR trials, unitless * `K`= Fulton's condition factor * `Relative Weight` = Body condition index, percentage **`Acute and Acclimated - Metabolic Rate Calculation`** folders contain the code used to process the raw data from AutoResp with the FishResp package in R. **`Acute-Metabolic Rate Calculation Code` -** Folder contains eight R scripts that were used for processing raw data obtain from experiments for acute respirometry experiments. The scripts utilize the .txt files located in in the Raw and Processed Respirometry Files folder and creates the .csv files located in those same folders.  * **`LP_BC_EXP1_8.3.2021.R`**- Code used to calculate metabolic rates for the first week of acute metabolic experiments for Walleye from the lower peninsula Bay City rearing pond * **`LP_BC_EXP2_8.30.2021.R`** - Code used to calculate metabolic rates for the second week of acute metabolic experiment for Walleye from the lower peninsula Bay City rearing pond * **`LP_DB_EXP1_9.6.2021.R`** -Code used to calculate metabolic rates for the first week of acute metabolic experiment for Walleye from the lower peninsula Dearborn rearing pond  * **`LP_DB_EXP2_9.13.2021.R`** -Code used to calculate metabolic rates for the second week of acute metabolic experiment for Walleye from the lower peninsula Dearborn rearing pond * **`UP_LF_EXP1_8.16.2021.R`** -Code used to calculate metabolic rates for the first week of acute metabolic experiment for Walleye from the upper peninsula Menominee rearing pond * **`UP_LF_EXP2_8.23.2021.R`** -Code used to calculate metabolic rates for the second week of acute metabolic experiment for Walleye from the upper peninsula Menominee rearing pond * **`27_ALLSTOCK_9.20.2021.R`** -Code used to calculate metabolic rates for the first week of high temperature acute metabolic experiment for Walleye from all rearing ponds * **`27_ALLSTOCK_EXP2_11.14.2021.R`** - Code used to calculate metabolic rates for the second week of high temperature acute metabolic experiment for Walleye from all rearing ponds **`Acclimated - Metabolic Rate Calculation Code` -**  Folder contains six R scripts that were used for processing raw data obtain from experiments for acute respirometry experiments. The scripts utilize the .txt files located in in the Raw and Processed Respirometry Files folder and creates the .csv files located in those same folders. * **`LP_BC_Acclimated_EXP1_10.10.2021.R` -** Code used to calculate metabolic rates from raw data files for the first week of Acclimated experiments using fish from the Bay City pond. File contains code for processing all temperature trials conducted that week. * **`LP_BC_Acclimated_EXP2_11.07.2021.R`-** Code used to calculate metabolic rates from raw data files for the second week of Acclimated experiments using fish from the Bay City pond. File contains code for processing all temperature trials conducted that week. * **`LP_DB_Acclimated_EXP1_10.17.2021.R`-** Code used to calculate metabolic rates from raw data files for the first week of Acclimated experiments using fish from the Dearborn pond. File contains code for processing all temperature trials conducted that week. * **`LP_DB_Acclimated_EXP2_10.31.2021.R`-** Code used to calculate metabolic rates from raw data files for the first week of Acclimated experiments using fish from the Dearborn pond. File contains code for processing all temperature trials conducted that week. * **`LP_LF_Acclimated_EXP1_10.3.2021.R`-** Code used to calculate metabolic rates from raw data files for the first week of Acclimated experiments using fish from the Dearborn pond. File contains code for processing all temperature trials conducted that week. * **`LP_LF_Acclimated_EXP2_10.25.2021.R`-** Code used to calculate metabolic rates from raw data files for the first week of Acclimated experiments using fish from the Dearborn pond. File contains code for processing all temperature trials conducted that week. **`Raw and Processed Respirometry Files From AutoResp`**` `- Contains raw and processed respirometry data in the form of .txt and .csv files produced through experiments outlined in the manuscript. .txt files contain raw oxygen measurements .csv files contain processed metabolic rates calculated from the raw oxygen measurements these data are unified in the **`Metabolism.Data.csv`** file that was used for manuscript analysis. Each Folder within this file is the date stamp of the start of an experiment, with each experiment being comprised of several different measurement periods. **Folders:** * **`Static MR_8.02.2021` -** First week of acute respirometry experiments with walleye from Bay City rearing pond. Contains 43 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_8.16.2021` -** First week of acute respirometry experiments with walleye from the Menominee rearing pond. Contains 42 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_8.23.2021`** - Second week of acute respirometry experiments with walleye from the Menominee rearing pond. Contains 39 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_8.30.2021`** - Second week of acute respirometry experiments with walleye from the Bay City rearing pond. Contains 45 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_9.06.2021`** - First week of acute respirometry experiments with walleye from the Dearborn rearing pond. Contains 39 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_9.13.2021`** - Second week of acute respirometry experiments with walleye from the Dearborn rearing pond. Contains 43 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_9.20.2021`** - First week of high temperature acute respirometry experiments with walleye from the all rearing ponds. Contains 62 .txt files generated from respirometry experiments. Contains six .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_10.03.2021`** - First week of acclimated respirometry experiments with walleye from the Menominee rearing pond. Contains 38 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_10.10.2021`** - First week of acclimated respirometry experiments with walleye from the Menominee rearing pond. Contains 37 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_10.17.2021`** - First week of acclimated respirometry experiments with walleye from the Dearborn rearing pond. Contains 37 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_10.24.2021`** - Second week of acclimated respirometry experiments with walleye from the Menominee rearing pond. Contains 39 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_10.31.2021`** - Second week of acclimated respirometry experiments with walleye from the Dearbon rearing pond. Contains 40 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_11.7.2021`** - Second week of acclimated respirometry experiments with walleye from the Bay City rearing pond. Contains 39 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. * **`Static MR_11.14.2021`** - Second week of high temperature acute respirometry experiments with walleye from the all three rearing pond. Contains 34 .txt files generated from respirometry experiments. Contains four .csv files that contain processed data from the experiment that were then used to populate the final data set. **File structure in `Acute and Acclimated - Metabolic Rate Calculation`** * *.txt files* contain the raw measurements of oxygen levels (% Saturation) in respirometry chambers. Files that contain *raw.txt* consist of the per second measurements whereas .txt files contain measurements consolidated into measurement cycles consisting of the waiting, closed, and flush period of the respirometry experiment.  They are divided into different segmentations of the experiment as described below. These files are subsequently used by the R scrips located in  **`Acute and Acclimated - Metabolic Rate Calculation`** folders. These files take on similar data file name structure across all folders. * `Acclimation` - Measurement of respirometry chambers while fish in experiment were acclimated to the respirometry system. No measurements were conducted during these time periods. * `empty_pre `- Measurement of background respiration rate prior to the start of experiments. * `empty_post` - Measurement of background respiration rate after the conclusion of experiments * `SMR_XX`- Measurements of Standard Metabolic Rate (SMR) used for manuscript XX in the file represents the temperature in celsius the measurements were made at * `MMR_XX` - Measurements of Maximum Metabolic Rate (MMR) used for manuscript XX in the file represents the temperature in celsius the measurements were made at * `tempchange_XX_YY`- Measurements during the temperature changes conducted during experiment XX represents starting temperature in celsius YY represents ending temperature * `converted` files are intermediate files used from taking the raw data in .txt files and converting oxygen measurements to metabolic rates utilizing the R package FishResp. * *.csv files*-Files names are structured as these files contain the calculated metabolic rates subsequently used in the analysis for the manuscript. Contain information on Temperature, slope of oxygen consumption curve, R2 used in metabolic rate calculation and mass and non-mass specific metabolic rates. File names for .csv files are of the structure-  Stock Pond Calculation Type Experiment Number. CSV * Stocks - LP, Lower Peninsula; UP, Upper Peninsula; All, all two stocks * Pond - BC, Bay City; DB, Dearborn; LF Menominee; All, all three ponds  * Calculation Type * Acute SMR- Calculations of Standard Metabolic Rate * Acute MMR - Calculations of Maximum Metabolic Rate from just the Chase Routine experiment * Acute SMR.MMR - Calculations of Maximum Metabolic Rate from just the period in which Standard Metabolic Rate was measured * MMR.Best - Highest Maximum Metabolic Rate achieved by fish through either the chase routine or the Standard Metabolic Rate measurement period * Experiment Number, EXP1, EXP2 - whether it was the first or second week of experiments Contents of processed .csv files: * `Chamber.No` = Which chamber 1-8 in the respirometry system fish were in during experiment * `Ind` = Unique identifier for fish, numerical * `Mass` = Wet mass (g) * `Volume` = Volume of respirometry chamber (mL) * `Date.Time` = yyyy-mon-dd hh:mm:ss * `Phase` = The type of phase and an ordinal number of measurement * `Temp` = Real time temperature in fish chamber (C) * `Slope.with.BR` = Decline in oxygen due to fish respiration and background respiration (mg02/L/s) * `Slope` = Decline in oxygen due to just fish respiration (mg02/L/s) * `SE` = Standard error of SMR (mg02/L/s) * `R2` = R2 used for calculating metabolic rate from oxygen decline slopes * `MR.abs.with.BR` = Combined respiration of fish and background * `BR` = Background respiration rate * `MR.abs` = mg02/min * `MR.mass` =  mg02/kg/h * `DO.Unit` = unit of DO concentration measurement * `Trial` = Whether measurement occurred during MMR trial or SMR trial * `Temperature` = Temperature as a factor (C) * `Event` = Numerical order of experiment events 1-4