DOI: 10.5061/dryad.j9kd51cr4
title: Data from: Statistical decomposition of passive and active phenotypic plasticity in traits under homeostatic regulation

description: 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.
description: # Data from: Statistical decomposition of passive and active phenotypic
 plasticity in traits under homeostatic regulation Dataset DOI:
 [10.5061/dryad.j9kd51cr4](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