Data from: Statistical decomposition of passive and active phenotypic plasticity in traits under homeostatic regulation
Data files
Jan 25, 2026 version files 2.48 MB
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data_references.txt
55.47 KB
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Mixed_plasticity.R
60.21 KB
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README.md
3.73 KB
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salinity_data.txt
2.36 MB
Abstract
Phenotypic plasticity enables organisms to maintain an optimal phenotype in the face of environmental change. Phenotypic plasticity is often viewed as being either passive or active. Yet many traits exhibit what we term mixed plasticity, where both passive effects of the environment and active physiological regulation shape trait dynamics. Indeed, this is a key characteristic of traits that are under homeostatic regulation, where organisms attempt to reverse environmental disturbance of the phenotype. Here, we develop a novel model that decomposes the temporal dynamics of homeostatic or mixed plasticity traits into parameters that describe the passive effect of the environment, the rate at which active regulation is adjusted (i.e., rate of plasticity), and the asymptotic magnitude of active regulation (i.e., capacity for plasticity). We apply this model to a dataset comprising 653 experiments documenting time-course changes in ion concentrations and osmolality in aquatic organisms following salinity shifts.
Dataset DOI: 10.5061/dryad.j9kd51cr4
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.
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
- species: scientific name of species studied
- page: page number of publication where data were found
- figure.table: figure or table number where the data were found
- according to.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
- . unit: unit of trait.value
- temperature: at what temperature the experiment was conducted
- mass.g.from.paper: mass in grams 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: Mixed_plasticity.R
Description: R script processing and analyzing the data given in "salinity_data.txt". This script cleans and standardizes salinity‐acclimation data, classifies traits and tissues, and keeps only “mixed plasticity” ion traits measured in comparable units.
It then fits a mechanistic time‐course model to each experiment to estimate regulation parameters, filters out non-regulating cases, and runs phylogenetically informed meta-analyses on the remaining experiments.
Code/software
The R script "Mixed plasticity.R" processes the raw data, estimates plasticity parameters based on these, and provides the statistical analyses of these.
Access information
Other publicly accessible locations of the data:
- DOI: 10.5061/dryad.r2280gbpx