Data from: Transgenerational epigenetic inheritance increases trait variation but is not adaptive
Data files
Apr 07, 2025 version files 540.57 KB
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Daphnia_TEI_240430.csv
426.01 KB
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Daphnia_TEI_Analysis_240221.R
63.46 KB
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Daphnia_TEI_PopulationDynamics_20240430.csv
45.36 KB
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README.md
5.74 KB
Abstract
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.
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 |
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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 |
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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 |
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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) |
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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 |
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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.csv. 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.