Data from: Plasticity rates and capacities differ across traits and temperatures: Insights from physiological responses of aquatic organisms to salinity change
Data files
Apr 02, 2025 version files 2.66 MB
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active_plasticity_bivariate_metaanalysis_v10.R
43.74 KB
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data_references.txt
55.47 KB
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Model_estimates.txt
193.99 KB
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README.md
6.72 KB
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salinity_data.txt
2.36 MB
Abstract
Phenotypic plasticity allows organisms to track changing trait optima under environmental variation. To what extent this is achieved will be jointly determined by the rate of and the capacity for plasticity. Despite the potential fitness implications of these two components of phenotypic plasticity, a quantitative understanding of their variance across trait types and environmental conditions is lacking. Here we address this knowledge gap by compiling data from previously published time-course experiments that describe how a range of physiological traits of aquatic ectotherms change in response to a shift in salinity. We then build upon recent analytical advances to produce estimates of plasticity rate and capacity from each experiment that are comparable across traits. A total of 324 estimates of plasticity rate and capacity originating from 59 species of fishes, sharks and crustaceans are given. The traits include histology, hormone concentrations, metabolite concentrations and metabolic and osmoregulatory enzyme activity.
Dataset DOI: 10.5061/dryad.r2280gbpx
Description of the data and file structure
A literature search was conducted to obtain a relatively comprehensive and representative sample of the published literature documenting the time-course of acclimation responses to salinity change in aquatic organisms. Such data come from experiments where organisms are first kept at one level of salinity before being abruptly shifted to a new salinity. Phenotypic measurements are taken at intervals from before the shift and for a certain period following this shift. These time series of measurements allows for estimation of both how much the phenotype changes (capacity), and the rate at which it changes.
Raw data are given in the file “salinity_data.txt”.
References to the data given in “salinity_data.txt” are given in the file “data references.docx”.
The R script “active_plasticity_bivariate_metaanalysis_v10.R” processes the raw data, estimates rates and capacities of plasticity based on these, and provides the statistical analyses of these.
For convenience we provide the estimated rates and capacities produced by the R script directly for users who want to utilize these estimates without going through the estimation procedures themselves. These estimates are given in the file “Model_estimates.txt”.
Missing values
Missing values in the data files are given as “NA”
Files and variables
File: salinity_data.txt
Description: Raw time-series data of phenotypic traits following a shift in salinity obtained from the publications
Variables
- experiment: Originally assigned experiment number (note that these are renumbered in the file Model_estimates.txt which comprises a smaller number of experiments that were selected for statistical analyses based on data characteristics)
- author: name of first author of publication
- year: year of publication
- title: title of publication
- speces: scientific name of species studied
- page: page number of publication where data were found
- figure.table: figure or table number where data were found
- acc.sal1: Salinity of water organisms experienced prior to a shift in salinity
- acc.sal1.duration.d: Duration of time (in days) the organisms were kept at a controlled salinity before being shifted
- acc.sal2: Salinity of water organisms experienced following the shift in salinity
- sal.unit: Unit in which acc.sal1 and acc.sal2 are given
- acc.type.control: whether salinity prior to the shift was controlled and reported (given by the value “pre”, all included studies in the database did this)
- tissue: what type of tissue the phenotypic trait was measured in’
- trait: what phenotypic trait was measured
- time: how long after the shift a trait measurement was conducted
- time.unit: unit of the value for “time”
- trait.value: measured value for the phenotypic trait
- trait.unit: unit of trait.value
- temperature: at what temperature the experiment was conducted
- mass.g.from.paper: mass in gram of organisms measured
- length.mm.from.paper: length in mm of organisms measured
- paper: First author name and year of publication
- acc.sal1.osm: osmolality of water prior to shift in salinity
- acc.sal2.osm: osmolality of water following shift in salinity
- direction: direction of change in salinity (increase or decrease)
- mintime: time of first phenotypic measurement, where 0 indicates prior to salinity shift (all included experiments did this).
File: data references.txt
Description: References for data given in “salinity_data.txt”
File: active_plasticity_bivariate_metaanalysis_v10.R
Description: R script processing and analysing the data given in “salinity_data.txt”.
File: Model_estimates.txt
Description: Estimated rates and capacities of phenotypic plastic responses based on the raw data given in the file salinity_data.txt
- species: scientific species name
- experiment: experiment number
- lambda: estimated rate of plasticity
- lambda.var: variance of the estimated rate of plasticity
- lFC.inf: capacity of plasticity
- lFC.inf.var: variance of the estimated rate of plasticity
- lFC.lambda.covar: covariance between estimated rate and capacity of plasticity
- peak.time: estimated breakpoint (in hours) for a segmented linear regression between time after a change in salinity and the trait value if the slope of the second segment was negative (i.e. the time at which a transient change in a trait reaches its peak). If second segment was positive the peak time equals the duration of the experiment.
- author: Name of first author of publication giving the data
- year: Year of publication giving the data
- title: Title of publication giving the data
- acc.sal1: Salinity of water organisms experienced prior to a shift in salinity
- acc.sal1.duration.d: Duration of time (in days) the organisms were kept at a controlled salinity before being shifted
- acc.sal2: Salinity of water organisms experienced following the shift in salinity
- sal.unit: Unit in which acc.sal1 and acc.sal2 are given
- acc.type.control: whether salinity prior to the shift was controlled and reported (given by the value “pre”, all included studies in the database did this)
- tissue: what type of tissue the phenotypic trait was measured in’
- trait: what phenotypic trait was measured
- trait.unit: unit of trait measurement
- temperature: at what temperature the experiment was conducted
- mass.g.from.paper: mass in gram of organisms measured
- length.mm.from.paper: length in mm of organisms measured
- paper: Name of first author and year of publication
- acc.sal1.osm: Osmolality of water organisms experienced prior to a shift in salinity
- acc.sal2.osm: Osmolality of water organisms experienced following the shift in salinity
- direction:direction of change in salinity (increase or decrease)
- mintime: time of first phenotypic measurement, where 0 indicates prior to salinity shift (all included experiments did this).
- maxtime: time (h) after salinity shift of final phenotypic measurement
- init.trait: value of first phenotypic measurement
- max.obs.trait: maximum observed trait value
- min.obs.trait: minimum observed trait value
- final.obs.value: trait value at final measurement
- nr.obs: number of observations (times) in an experiment
- trait.type: type of trait measured, categorized
- plasticity.type: type of plasticity response (all plastic responses that were included in statistical analyses were considered to be active)
- class: taxonomic class of species