Data from: Increased temperature decreases starvation resiliency in first feeding sablefish (Anoplopoma fimbria)
Data files
Jul 09, 2026 version files 56.54 KB
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DFI.df.rda
1.60 KB
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mean_log_morpho_dat.start_YS_nona.rda
12.49 KB
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mean_log_morpho_matrix_YS.rda
12.43 KB
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mean_sf.length.df.analysis_int.rda
2.09 KB
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morpho_dat.start_YS_Ellipse_mean.rda
1.84 KB
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README.md
10.79 KB
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scores_mean_log_nmds_YS_no9B.rda
15.31 KB
Abstract
Waters in the Gulf of Alaska experienced anomalously high temperatures during a recent outbreak of large marine heatwaves (2014-2016 and 2019). These warming events caused shifts in the reproductive phenology of zooplankton and fish species, potentially creating trophic mismatches between the availability of zooplankton prey and the initiation of larval fish feeding. To better understand the implications of warming-induced trophic mismatches on sablefish (Anoplopoma fimbria) starvation resiliency, we reared larval sablefish in the laboratory under two temperature treatments (6 °C & 9 °C) with two nested feeding treatments (fed & starved). We measured the point of no return, daily larval length, weight, and yolk sac size trajectories, and body morphometrics. Sablefish larvae experienced an 11-day decrease in time to reach point of no return at 9 °C, diverging length and weight trajectories between starved and fed larvae at 9 °C, smaller yolk sac size at first feeding and earlier depletion at 9 °C, and changes in skull morphology between temperature and feeding treatments. These results indicate that sablefish starvation resiliency greatly decreases under anomalous warming in the Gulf of Alaska.
Dataset DOI: 10.5061/dryad.mpg4f4rfj
Description of the data and file structure
The following data were used in analyses to determine the starvation resiliency of larval sablefish under elevated temperature conditions.
DFI.df.rda: these data contain daily feeding incidence and group weight values and were used to plot mean daily feeding incidence to determine the point of no return for larval sablefish in the replicate temperature treatments. The R script "Point of No Return Analysis.R" was used to perform this analysis. Additionally, these data were used to analyze how mean daily weight trajectories vary by temperature and feeding treatments in the R script "Weight GAMM Analysis.R".
sf.length.df.analysis.rda: these data contain length measurements for larval sablefish collected from each temperature and feeding treatment replicate. These data are used in the R script "Length GAMM Analysis.R" to analyze how mean daily length trajectories vary by temperature and feeding treatments.
morpho_dat.start_YS_Ellipse_mean.rda: these data contain morphometric measurement of individual larval sablefish and were used to evaluate how yolk sac area varies with temperature and feeding treatments. This analysis was performed in the R script "Yolk Sac Analysis.R".
mean_log_morpho_dat.start_YS_nona.rda: These data contain morphometric measurements of larval sablefish that have been normalized to a mean of 0 and standardized by individual fish length before being averaged across all individual in a given treatment on a particular experimental day. These data are used in combination with mean_log_morpho_matrix_YS.rda and the R script "NMDS Analysis Script.R" to analyze how mean daily morphometric traits vary among temperature and feeding treatments, as well as between yolk sac and pre-flexion life stages.
scores_mean_log_nmds_YS_no9B.rda: These data are the scores that resulted from the nmds analyses of morphological traits. These scores were then used in the R script "Decision Tree Analysis.R" that perform regression tree analyses to identify the main morphological differences between larvae reared in the different temperature and feeding treatments.
Files and variables
File: DFI.df.rda
Description: These data were collected to capture changes in daily feeding incidence (DFI) and weight across the different experimental temperature treatments (Temp) and feeding treatments (Fed). DFI was scored as either feeding (1) or not feeding (0) based on the presence/absence of food in the guts of larval sablefish. Weights were measured for groups of 2-5 larvae and each larva in a group was assigned the mean weight of the group. Up to 15 individuals in a given temperature x feeding treatment were assessed for DFI and weight each day (exp_day). Mean DFI and weight were calculated for each experimental day. Feeding trials for the 6 °C treatment were run in 2022 while the 9 °C trials were run in 2023. Mean DFI was plotted daily and when the DFI of the starved treatment was less than 50% of the fed treatment on a clear downward trajectory (from a Generalized Linear Model fit), the starved treatment had reached the point of no return.
Variables
- Year
- Replicate (Rep)
- Feeding Treatment (Fed)
- Experimental Day (exp_day)
- Daily Feeding Incidence (DFI; proportion)
- Weight (weight; mg)
- Temperature Treatment (Temp; degrees Celsius)
- Treatment combination used for analyses and plotting (class)
File: mean_sf.length.df.analysis_int.rda
Description: This data frame contains mean and standard deviation values of daily length measurements for larval sablefish in the different treatments/replicates. This data set is used to test a suite of model configurations to determine which model best explains variability in sablefish length trajectories and explores the ways in which temperature, feeding treatment, and replicate affect length trajectories.
Variables
- Experimental Day (exp_day)
- Temperature Treatment (Temp; degrees Celsius)
- Feeding Treatment (Fed)
- Replicate (Rep)
- Mean length (mean_length; in mm)
- Standard deviation of length (sd_length)
File: mean_log_morpho_dat.start_YS_nona.rda
Description: These data were collected to examine changes in larval sablefish body and skull morphology through time in the different temperature and feeding treatments. Based on the presence of absence of a yolk sac, larvae where categorized into either Yolk Sac or Pre-Flexion (yolk sac absorbed) life stages. Individual larvae were imaged under a stereomicroscope and, using Image Pro 10, had 11 morphometric measurements taken. These measurements were then log transformed and then averaged for each temperature x feeding treatment x replicate x life stage x experimental day. These mean measurements were then used in Non-metric dimensional scaling analysis to determine how changes in morphological traits varied across temperature and feeding treatments throughout the experiment.
Variables
- Temperature Treatment (Temp; degrees Celsius)
- Replicate (Rep)
- Feeding Treatment (Fed)
- Life stage (YS)
- Experimental Day (exp_day)
- mean notochord length (mean NL; mm)
- mean head length (meanHL; mm)
- mean eye diameter (meanED; mm)
- mean head height (meanHH; mm)
- mean body depth at pectorals (meanBDP; mm)
- mean body depth at anus (meanBDA; mm)
- mean gut length (meanGL; mm)
- mean yolk sac length (meanYSL; mm)
- mean yolk sac depth (meanYSD; mm)
- mean upper jaw length (meanUJL; mm)
- mean lower jaw length (meanLJL; mm)
- treatment by day identification number (ID)
File: mean_log_morpho_matrix_YS.rda
Description: Matrix of the mean daily morphometric measurements that had been log transformed. These data are used to create the distance matrix used in the NMDS. The row numbers are the ID values from mean_log_morpho_dat.start_YS_nona.rda. These ID values were used to combine the scores data from the NMDS with the original treatment information so we could make inferences about how morphological traits varied by treatment, experimental day, and life stage.
Variables
- mean notochord length (mean NL; mm)
- mean head length (meanHL; mm)
- mean eye diameter (meanED; mm)
- mean head height (meanHH; mm)
- mean body depth at pectorals (meanBDP; mm)
- mean body depth at anus (meanBDA; mm)
- mean gut length (meanGL; mm)
- mean yolk sac length (meanYSL; mm)
- mean yolk sac depth (meanYSD; mm)
- mean upper jaw length (meanUJL; mm)
- mean lower jaw length (meanLJL; mm)
File: morpho_dat.start_YS_Ellipse_mean.rda
Description: This data frame contains daily mean yolk sac ellipse area and standard error data. It is used to analyze how daily trajectories of yolk sac area vary by temperature and feeding treatments across replicates.
Variables
- Experimental Day (exp_day)
- Feeding Treatment (Fed)
- Temperature Treatment (Temp; degrees Celsius)
- Replicate (Rep)
- Sample size (n)
- Mean Ellipse Area (mean_Ellipse_Area; mm)
- Standard Error of Ellipse Area (SE_Ellipse_Area)
- Treatment combination used for analyses and plotting (class)
File: scores_mean_log_nmds_YS.rda
Description: Scores from NMDS looking at the effects of temperature treatment, feeding treatment, experimental day, and replicate on morphological traits as well as the individual log transformed morphological trait measurements. These data were used in decision tree analysis to determine which morphological traits varied between temperature and feeding treatments.
Variables
- ID
- NMDS1 Scores (NMDS1)
- NMDS2 Scores (NMDS2)
- Temperature Treatment (Temp; degrees Celsius)
- Replicate (Rep)
- Feeding Treatment (Fed)
- Life stage (YS)
- Experimental Day (exp_day)
- Mean notochord length (meanNL; mm)
- Mean head length (meanHL; mm)
- Mean eye diameter (meanED; mm)
- Meanhead height (meanHH; mm)
- Mean body depth at pectorals (meanBDP; mm)
- Mean body depth at anus (meanBDA; mm)
- Mean gut length (meanGL; mm)
- Mean yolk sac length (meanYSL; mm)
- Mean yolk sac depth (meanYSD; mm)
- Mean upper jaw length (meanUJL; mm)
- Mean lower jaw length (meanLJL; mm)
- Treatment combination used for analyses and plotting(class)
Code/software
The following R scripts (R version 4.3.1) were used for data analysis and plotting and are located at https://doi.org/10.5281/zenodo.21269843:
Point of No Return Analysis: this script takes daily feeding incidence data from DFI.df.rda to plot mean daily feeding incidence for each temperature by feeding treatment replicate. It requires the packages dplyr and ggplot2.
Length GAMM Analysis: This script takes data from mean_sf.length.df.analysis_int.rda to test a variety of Hierarchical Generalized Additive Model configurations examining the influence of temperature, feeding treatment, and replicate on daily length trajectories. It then ranks the models by AIC, evaluates the model fit of the best model, and plots the partial effects of the treatments on length trajectories. It requires the packages mgcv, dplyr, and ggplot2.
Weight GAMM Analysis: This script takes data from DFI.df.rda to test a variety of Hierarchical Generalized Additive Model configurations examining the influence of temperature, feeding treatment, and replicate on daily length trajectories. It then ranks the models by AIC, evaluates the model fit of the best model, and plots the partial effects of the treatments on length trajectories. It requires the packages mgcv, dplyr, and ggplot2.
Yolk Sac Analysis: This script takes data from morpho_dat.start_YS_Ellipse_mean.rda to test a variety of linear models examining the effects of temperature treatment, feeding treatment, experimental day, and replicate on yolk sac area trajectories. It requires the packages tidyverse, vegan, and ggplot2.
NMDS Analysis Script: This script takes data from mean_log_morpho_dat.start_YS_nona.rda and mean_log_morpho_matrix_YS.rda to run a non-metric multidimensional scaling analysis to determine how morphometric measurements vary by temperature treatment, feeding treatment, life stage, and replicate. It requires the packages tidyverse, vegan, RColorBrewer, Hmisc, corrplot, and ggplot2.
Decision Tree Analysis : This script takes data from scores_mean_log_nmds_YS_no9B.rda and runs a decision tree examining the morphological features that differ between temperature treatments and the features that differ between feeding treatments. It requires the packages rpart, partykit, rpart.plot, caret, Metrics, and randomForest.