DOI: 10.5061/dryad.ffbg79d31
title: Data from: Transgenerational epigenetic inheritance increases trait variation but is not adaptive

description: Understanding organismal responses to environmental change is a central
 goal of biology with profound implications for the conservation of
 biodiversity. Widespread evidence of epigenetic modifications in response
 to environmental stress, including those inherited across generations, has
 led to considerable speculation about their role in organismal responses
 to environmental change. Yet, the magnitude and fitness consequences of
 epigenetic marks carried beyond maternal inheritance are largely unknown.
 Here, we tested how transgenerational epigenetic inheritance (TEI) shapes
 the phenotypic response of Daphnia clones to the environmental stressor
 Microcystis. We split individuals from each of eight genotypes into
 exposure and control treatments (P0 generation) and tracked the fitness of
 their descendants to the F3 generation. We found transgenerational
 epigenetic exposure to Microcystis led to reduced survival and growth
 rates and no consistent effect on offspring production. TEI was associated
 with increases in trait variance, suggesting the potential for heritable
 bet hedging driven by TEI. Taken together, our results demonstrate that
 TEI causes substantial—but not adaptive—trait shifts, suggesting
 transgenerational adaptive plasticity may be rare.
description: # Data from: Transgenerational epigenetic inheritance increases trait
 variation but is not adaptive
 [https://doi.org/10.5061/dryad.ffbg79d31](https://doi.org/10.5061/dryad.ffbg79d31) The dataset includes the R code and .csv files necessary to reproduce the statistical analyses and figures found in the manuscript "Transgenerational epigenetic inheritance increases trait variation but is not adaptive". ## Description of the data and file structure The .csv files are structured in table format with proper headings. The headings describe the specimen, generation times, treatments, and phenotypes measured in the transgenerational epigenetic inheritance study. Any missing values (empty cells) are replaced with an "N/A". Complete definitions of each heading is provided below: | Key | Description | | :---------- | :---------------------------------------------------------------------------- | | clone | Identity of daphnia (i.e., 1, 2, 3, 4, 5, 6, 7, 8) | | gen | Generation of daphnia (i.e., f0, f1, f2, f3) | | exposure | Generation of exposure to chlorella (C) or microcystis (M) (e.g., cccm, mccm) | | replicate | Number | | alive\_day7 | Alive (1=Y; 0=N) daphnia on day 7 | | dead\_day7 | Dead (1=Y; 0=N) daphnia on day 7 | | alive\_dayX | Alive (1=Y; 0=N) daphnia when first brood occurred (i.e., day X) | | dead\_dayX | Dead (1=Y; 0=N) daphnia when first brood occurred (i.e., day X) | | Fbrood | The time (in days) when the first brood occurred | | InvFbrood | The inverse time (d-1) when first brood occurred (i.e., maturation rate) | | neonates | Number of neonates produced per daphnia | | eye\_dayX | Eye size of daphnia when first brood occurred (i.e., day X) | | size\_day0 | Size (in mm) of daphnia on day 0 | | size\_day3 | Size (in mm) of daphnia on day 3 | | :-------------- | :------------------------------------------------------------------------------------------------------------------ | | size\_day7 | Size (in mm) of daphnia on day 7 | | size\_dayX | Size (in mm) of daphnia on day when first brood occurred (i.e., day X) | | growth\_day0to7 | Growth from day 0 to 7 (i.e., 'bodysize\_day7' - 'bodysize\_day0'; in mm) | | growth\_day0toX | Growth from day 0 to X, the day when daphnia had its first brood (i.e., 'bodysize\_dayX' - 'bodysize\_day0'; in mm) | | **days\_alive** | Total number of days alive | | :---------------- | :------------------------------------------ | | day0-28\_survival | Daily survival (1=alive; 0=dead) of daphnia | | survival\_day0 | Alive (1=Y; 0=N) daphnia on day 0 | | survival\_day3 | Alive (1=Y; 0=N) daphnia on day 3 | | survival\_day7 | Alive (1=Y; 0=N) daphnia on day 7 | | survival\_dayX | Alive (1=Y; 0=N) daphnia on day when first brood occurred (i.e., day X) | | :------------------------------------- | :------------------------------------------------------------------------------------- | | fertility\_day0 | Number of neonates produced per daphnia on day 0 | | fertility\_day3 | Number of neonates produced per daphnia on day 3 | | fertility\_day7 | Number of neonates produced per daphnia on day 7 | | fertility\_dayX | Number of neonates produced per daphnia on day when first brood occurred (i.e., day X) | | days\_to\_first\_reproduction | The time (in days) when the first brood occurred | | inverse\_days\_to\_first\_reproduction | The inverse time (d-1) when first brood occurred (i.e., maturation rate) | | bodysize\_day0 | Size (in mm) of daphnia on day 0 | | bodysize\_day3 | Size (in mm) of daphnia on day 3 | | bodysize\_day7 | Size (in mm) of daphnia on day 7 | | :------------- | :--------------------------------------------------------------------- | | bodysize\_dayX | Size (in mm) of daphnia on day when first brood occurred (i.e., day X) | There are two .csv files: **Daphnia_TEI_240430.csv** and **Daphnia_TEI_PopulationDynamics_20240430.cs**v. The first file is used for the statistical analyses and plot generations for Figure 2, Figure 3, and Figure S1. The second file is used for the statistical analyses and plot generations for Figure 4, Figure S2, and Figure S3. There is one .R code file: Daphnia_TEI_Analysis_241224.R. This file utilizes all three .csv files to run the statistical analyses and generate plots found in the manuscript "Transgenerational epigenetic inheritance increases trait variation but is not adaptive". ## Code/Software All statistical analyses were completed in R version 4.2.2.