Data and analyses from: Context matters: A meta-analysis of the variable impacts of transgenerational and developmental plasticity on responses to stress
Data files
Jan 07, 2025 version files 6.08 MB
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cleaned_Design_A_12.21.24.csv
1.90 MB
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cleaned_Design_B_12.21.24.csv
1.02 MB
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Design_A_lnRR_Spp.csv
2.05 MB
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Design_B_lnRR_Spp.csv
1.05 MB
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README.md
55.86 KB
Abstract
Understanding organisms’ abilities to adapt and acclimate to stressors in their environments is essential for predicting the distributions and persistence of species and populations during environmental change. Beyond genetic adaptation, prior experiences with a given stressor across life stages can dictate how an individual will fare when exposed to that stressor again. There is now a robust literature on the impacts of parental experiences on offspring traits (transgenerational plasticity), plus an even broader literature on the carry-over effects of early-life experience on phenotypic outcomes (within-generational or developmental plasticity); however, less is understood about the relative strengths of these two forms of plasticity and how they interact in shaping stress tolerance.
We explored these questions by conducting a meta-analysis of peer-reviewed studies that tested both within- and transgenerational effects of naturally occurring environmental stressors. All included studies featured clear “control” and “stress” treatments and a fully factorial design across both parents and offspring. We performed meta-regressions with contextual moderators including the traits measured, the type of stressor, taxonomic group, and organismal life history traits to elucidate patterns and develop a predictive framework for when we should expect to see effects of transgenerational plasticity, within-generational plasticity, both, or neither, and under what conditions we may find legacy effects to be adaptive or maladaptive.
We found that there was not a strong, overall effect of either parental or early-life exposure on subsequent offspring performance. However, experimental context (what stressor was used and what traits were measured) as well as biological context (taxonomy, life history traits) were important predictors for understanding the strength and direction of plasticity. We found several contexts where there were meaningful effects of parental and early-life stress exposure and evidence that these may interact to impact phenotypic and fitness outcomes.
Our study highlights the need for careful consideration of context when exploring patterns of plasticity. We hope to underscore the need for additional, fully factorial studies that measure the interaction between these forms of plasticity across a variety of systems and stressors to better understand how stress may carry forward across life stages and generations.
README: Data and analyses from: Transgenerational and Developmental Plasticity Both Shape Patterns of Environmental Stress Tolerance: A Meta-Analysis
https://doi.org/10.5061/dryad.d2547d8bw
Description of the data and file structure
This dataset was collected from published research papers as part of a meta-analysis examining the effects of transgenerational and developmental plasticity on organism stress tolerance. Raw data was collected from published manuscripts that fit a pre-determined set of criteria from either 1) raw data provided by authors in a repository or via personal communication, 2) data presented in tables, 3) data mined using the MetaDigitise package in R from figures. These raw data were then analyzed using a meta-analytic model and a series of meta-regression models to determine factors/moderators that significantly contributed to patterns in offspring trait measures. We used two designs and analyzed them separately. The aim for Design A was to determine if there were significant effects of parental treatment (transgenerational plasticity) and offpspring early-life treatment (developmental plasiticity) and their potential interactions on later offspring traits. The aim for Design B was to determine if the timing of parental exposure to stress (in early life or later in life) impacted transgenerational patterns.
Files and variables
Description of the data and files and structure
Design A Data
Data from all Design A studies included in the meta-analysis and prepared for R analyses.
Files: cleaned_Design_A_11.21.24.csv, Design_A_lnRR_Spp.csv
Code: Meta-analysis_Analysis_Design A_11.21.24.Rmd & MetaAnalysis_DesignA_FIGURES_11.29.24
cleaned_Design_A_11.21.24.csv
The raw data used in Design A analyses.
1. Number of variables: 50
2. Number of cases/rows: 789
Variable list (*denotes used or described in analyses presented in manuscript):
Source - Database where the study was found - Scopus, WoS (Web of Science), or Both (study found on both Scopus and Web of Science)
Record Number - A unique number given to each study prior to the first screening
*Study_ID - A unique number given only to studies used in the final analyses (studies that made it past the first and second screening), formatted as "S#"
*Effect_size_ID - A unique number given to each effect size calculated from studies included in the final analysis, formatted as "E#"
Authors - The authors of the study (full last name, first letter of first name only)
Authors_FullName - The authors of the study (full last name, full first name)
Title - Study title
Abstract - Study abstract
Journal - Journal where study was published
Year - Year study was published
Author_Keyword - Keywords provided by authors (empty cells indicate that keywords were not provided upon download from database)
DOI - The digital object identifier of the study
DOI_Link - The address with the digital object identifier that links to the article
*Species - The genus and species used in the study (Genus_species)
Population - Indicates if multiple populations/strains/sexes/groups were used in the study. "1" indicates that only one group was used, all other entries are taken from the study directly. Males and females were included separately only if the study specifically reported different results for each.
Lab_Wild - Whether the study species were reared in the lab/lab strains or taken from the wild ("lab" or "wild"). Species were considered wild if <2 generations were reared in the lab prior to the start of the study (e.g., if the study lab-acclimated the grandparental generation prior to creating the experimental parent generation, those were considered "wild").
Taxonomy - The broad taxonomic group the study species belongs to (1_invertebrates, 2_vertebrates, 3_annual_plants, 4_perennial_plants)
*Taxonomy_simple - There were very few studies using plants so we collapsed category 3 and 4 (perennial and annual plants) into just "plant" (1_invertebrates, 2_vertebrates, 3_plants)
Stressor*from*paper - The stressor used in the experiments using the exact wording from the study
*Stressor_Category - Grouping stressors by more general categories (1_Temperature, 2_Chemistry, 3_Resource quality, 4_Species interaction, 5_Infection)
Stressor_type - Broadest category of stressor, either biotic or abiotic (1_Biotic, 2_Abiotic)
*Transmission_type - Which parent(s) were experimentally manipulated (1_Biparental, 2_maternal, 3_paternal)
Timing_P - The life stage parents were experimentally manipulated in the study (1_Early-life, 2_Adult, 3_Both)
Timing_O1 - The life stage when the offspring early-life treatment/manipulation was administered (1_Embryo/Egg/Seed, 2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
*Timing_O2 - The life stage when the offspring later life trait measure was taken (2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
*Devo_traits - The developmental mode of the study species, either direct development or biphasic development (1_Biphasic, 2_Direct)
Life_history_traits - The reproductive life history traits of the study species (1_Internal gestation, 2_External embryos, 3_External gametes, 4_clonal)
Mobility_Juvenile - The mobility of the juvenile phase of the organism (1_Sessile, 2_Mobile)
Mobility_Adult - The mobility of the adult phase of the organism (1_Sessile, 2_Mobile)
Trait*_*from_paper - The trait being measured in the offspring with the wording taken directly from the study
Trait_Category - Traits grouped by more general categories (e.g., Mass/Weight, Length/Size, Survival, Metabolism/respiration, etc.)
*Trait_Type - Traits grouped into six broad categories (1_Physiology, 2_Morphology, 3_Life_history, 4_Survival, 5_Reproductive, 6_Behavior)
Trait_Unit - The unit of measurement of the trait (e.g., mm, g, seconds, etc.)
Negative*_*fitness_Correlation - Whether or not the trait has a negative correlation with fitness (i.e., a lower value is actually better, for example development time or latency to feed). For these traits, we reversed their sign to better understand our results as adaptive/maladative. A "0" indicates no correction was applied, a "1" indicates that the sign was reversed.
*Error_Imputed - Whether or not the trait measures lacked an error term and therefore had to be imputed (see Methods). A "0" indicates that the traits had error terms reported, a "1" indicates that the error term was imputed.
*Continuous_correction_applied - Whether or not a continuous correction was applied. For some studies, the mean or error term was equal to zero which cannot be used correctly in our effect size calculations so a continuous correction of 0.5 was applied to all values in that pairwise comparison (see Methods). A "0" indicates that no correction was applied, a "1" indicates that a continuous correction was applied.
*P_treatment - The treatment ("control" or "stress") of the parent
*O1_treatment - The treatment ("control" or "stress") of the offspring during their early life stage
*O2_treatment - The treatment ("control" or "stress") of the later life offspring stage during their trait measurement (e.g., "control" if lengths were measured in control conditions, "stress" if offspring were exposed to temperature stress and their tolerance measured as the trait of interest)
Treatment_combo - All three treatment moderators (P_treatment _ O1_treatment _ O2_treatment) combined into one term (for graphing purposes)
Offspring_combo - The two offspring treatment moderators (O1_treatment _ O2_treatment) combined into one term (for graphing purposes)
P_O1_combo - The parental and early-life offspring treatment moderators (P_treatment _ O1_treatment ) combined into one term (for graphing purposes)
*A_n_control - Sample size of the control treatment
*B_n_stress - Sample size of the stress treatment
*A_avg_control - The mean trait value of the control treatment
*B_avg_stress - The mean trait value of the control treatment
*A_sd_control - The standard deviation around the mean trait value of the control treatment
*B_sd_stress - The standard deviation around the mean trait value of the control treatment
NOTES - Additional notes or comments
3. Missing data codes: Only the "Author_Keywords" and "NOTES" columns should have blank cells, blank cells indicate information not retrieved or no additional information necessary
4. Specialized formats or abbreviations used:
P = parent
O = offspring
Design_A_lnRR_Spp.csv
The output after calculating effect sizes, imputing error terms, and assigning species and taxonomy in R (see Meta-analysis_Analysis_Design A_12.19.24.Rmd, csv file written from the matrix constructed in R).
1. Number of variables: 67
2. Number of cases/rows: 789
Variable list (*denotes used or described in analyses presented in manuscript):
ID - Unique number assigned to each row
*Species - The genus and species used in the study (Genus_species)
Source - Database where the study was found - Scopus, WoS (Web of Science), or Both (study found on both Scopus and Web of Science)
Record Number - A unique number given to each study prior to the first screening
*Study_ID - A unique number given only to studies used in the final analyses (studies that made it past the first and second screening), formatted as "S#"
*Effect_size_ID - A unique number given to each effect size calculated from studies included in the final analysis, formatted as "E#"
Authors - The authors of the study (full last name, first letter of first name only)
Authors_FullName - The authors of the study (full last name, full first name)
Title - Study title
Abstract - Study abstract
Journal - Journal where study was published
Year - Year study was published
Author_Keyword - Keywords provided by authors (empty cells indicate that keywords were not provided upon download from database)
DOI - The digital object identifier of the study
DOI_Link - The address with the digital object identifier that links to the article
Population - Indicates if multiple populations/strains/sexes/groups were used in the study. "1" indicates that only one group was used, all other entries are taken from the study directly. Males and females were included separately only if the study specifically reported different results for each.
Lab_Wild - Whether the study species were reared in the lab/lab strains or taken from the wild ("lab" or "wild"). Species were considered wild if <2 generations were reared in the lab prior to the start of the study (e.g., if the study lab-acclimated the grandparental generation prior to creating the experimental parent generation, those were considered "wild").
Taxonomy - The broad taxonomic group the study species belongs to (1_invertebrates, 2_vertebrates, 3_annual_plants, 4_perennial_plants)
*Taxonomy_simple - There were very few studies using plants so we collapsed category 3 and 4 (perennial and annual plants) into just "plant" (1_invertebrates, 2_vertebrates, 3_plants)
Stressor*from*paper - The stressor used in the experiments using the exact wording from the study
*Stressor_Category - Grouping stressors by more general categories (1_Temperature, 2_Chemistry, 3_Resource quality, 4_Species interaction, 5_Infection)
Stressor_type - Broadest category of stressor, either biotic or abiotic (1_Biotic, 2_Abiotic)
*Transmission_type - Which parent(s) were experimentally manipulated (1_Biparental, 2_maternal, 3_paternal)
Timing_P - The life stage parents were experimentally manipulated in the study (1_Early-life, 2_Adult, 3_Both)
Timing_O1 - The life stage when the offspring early-life treatment/manipulation was administered (1_Embryo/Egg/Seed, 2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
*Timing_O2 - The life stage when the offspring later life trait measure was taken (2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
*Devo_traits - The developmental mode of the study species, either direct development or biphasic development (1_Biphasic, 2_Direct)
Life_history_traits - The reproductive life history traits of the study species (1_Internal gestation, 2_External embryos, 3_External gametes, 4_clonal)
Mobility_Juvenile - The mobility of the juvenile phase of the organism (1_Sessile, 2_Mobile)
Mobility_Adult - The mobility of the adult phase of the organism (1_Sessile, 2_Mobile)
Trait*_*from_paper - The trait being measured in the offspring with the wording taken directly from the study
Trait_Category - Traits grouped by more general categories (e.g., Mass/Weight, Length/Size, Survival, Metabolism/respiration, etc.)
*Trait_Type - Traits grouped into six broad categories (1_Physiology, 2_Morphology, 3_Life_history, 4_Survival, 5_Reproductive, 6_Behavior)
Trait_Unit - The unit of measurement of the trait (e.g., mm, g, seconds, etc.)
Negative*_*fitness_Correlation - Whether or not the trait has a negative correlation with fitness (i.e., a lower value is actually better, for example development time or latency to feed). For these traits, we reversed their sign to better understand our results as adaptive/maladative. A "0" indicates no correction was applied, a "1" indicates that the sign was reversed.
*Error_Imputed - Whether or not the trait measures lacked an error term and therefore had to be imputed (see Methods). A "0" indicates that the traits had error terms reported, a "1" indicates that the error term was imputed.
*Continuous_correction_applied - Whether or not a continuous correction was applied. For some studies, the mean or error term was equal to zero which cannot be used correctly in our effect size calculations so a continuous correction of 0.5 was applied to all values in that pairwise comparison (see Methods). A "0" indicates that no correction was applied, a "1" indicates that a continuous correction was applied.
*P_treatment - The treatment ("control" or "stress") of the parent
*O1_treatment - The treatment ("control" or "stress") of the offspring during their early life stage
*O2_treatment - The treatment ("control" or "stress") of the later life offspring stage during their trait measurement (e.g., "control" if lengths were measured in control conditions, "stress" if offspring were exposed to temperature stress and their tolerance measured as the trait of interest)
Treatment_combo - All three treatment moderators (P_treatment _ O1_treatment _ O2_treatment) combined into one term (for graphing purposes)
Offspring_combo - The two offspring treatment moderators (O1_treatment _ O2_treatment) combined into one term (for graphing purposes)
P_O1_combo - The parental and early-life offspring treatment moderators (P_treatment _ O1_treatment ) combined into one term (for graphing purposes)
*A_n_control - Sample size of the control treatment
*B_n_stress - Sample size of the stress treatment
*A_avg_control - The mean trait value of the control treatment
*B_avg_stress - The mean trait value of the control treatment
*A_sd_control - The standard deviation around the mean trait value of the control treatment
*B_sd_stress - The standard deviation around the mean trait value of the control treatment
NOTES - Additional notes or comments
*lnRR - Effect size calculated using a log response ratio with correction (see Equation 1 in Methods)
*lnRRV - Variance around the effect size, sampling variance (see Equation 2 in Methods)
*Precision - The inverse of the standard error (or 1/SQRT(lnRRV))
cv_control - [part of error imputation calculations] The coefficient of variation for the control treatments using all effect sizes that are NOT missing error terms.
cv_stress - [part of error imputation calculations] The coefficient of variation for the stress treatments using all effect sizes that are NOT missing error terms.
b_CV2_1 - [part of error imputation calculations] The average between-study coefficient of variation (CV) in control treatments.
b_CV2_2 - [part of error imputation calculations] The average between-study coefficient of variation (CV) in stress treatments.
cv2_control_new - [part of error imputation calculations] A column where values for effect sizes that have error terms keep their values (cv_control) or if they are missing error terms we insert the weighted between-study CV to replace missing CV (which is due to missing SD) for control treatments.
cv2_stress_new - [part of error imputation calculations] A column where values for effect sizes that have error terms keep their values (cv_control) or if they are missing error terms we insert the weighted between-study CV to replace missing CV (which is due to missing SD) for control treatments.
lnRR_new - [output of error imputation calculations for those missing data] The new point estimate of lnRR using either the between-individual CV^2 when missing or normal CV^2 when not missing. For both lnRR and lnRRV, we merged the columns so that these new values became the lnRR and lnRRV values for those missing error terms (imputed) while the original values were kept for those that had an error term.
lnRRV_new - [output of error imputation calculations for those missing data] The new point estimate of lnRRV (sampling variance) using either the between-individual CV^2 when missing or normal CV^2 when not missing. For both lnRR and lnRRV, we merged the columns so that these new values became the lnRR and lnRRV values for those missing error terms (imputed) while the original values were kept for those that had an error term.
db - The database the* taxize* package used to assign taxonomic information to each species (all were ncbi).
phylum - Phylum of the study species.
class - Class of the study species.
order - Order of the study species.
family - Family of the study species.
3. Missing data codes: Only the "Author_Keywords" and "NOTES" columns should have blank cells, blank cells indicate information not retrieved or no additional information necessary
4. Specialized formats or abbreviations used:
P = parent
O = offspring
lnRR = effect size (using log response ratio)
lnRR = sampling variance
CV = coefficient of variation
Design B Data
Data from all Design B studies included in the meta-analysis and prepared for R analyses.
Files: cleaned_Design_B_11.21.24.csv; Design_B_lnRR_Spp.csv
Code: Meta-analysis_Analysis_Design B_11.17.24.Rmd & MetaAnalysis_DesignB_FIGURES_11.29.24
cleaned_Design_B_11.21.24.csv
1. Number of variables: 47
2. Number of cases/rows: 392
Variable list (*denotes used or described in analyses presented in manuscript):
Source - Database where the study was found - Scopus, WoS (Web of Science), or Both (study found on both Scopus and Web of Science)
Record Number - A unique number given to each study prior to the first screening
*Study_ID - A unique number given only to studies used in the final analyses (studies that made it past the first and second screening), formatted as "S#"
*Effect_size_ID - A unique number given to each effect size calculated from studies included in the final analysis, formatted as "E#"
Authors - The authors of the study (full last name, first letter of first name only)
Authors_FullName - The authors of the study (full last name, full first name)
Title - Study title
Abstract - Study abstract
Journal - Journal where study was published
Year - Year study was published
Author_Keyword - Keywords provided by authors (empty cells indicate that keywords were not provided upon download from database)
DOI - The digital object identifier of the study
DOI_Link - The address with the digital object identifier that links to the article
*Species - The genus and species used in the study (Genus_species)
Population - Indicates if multiple populations/strains/sexes/groups were used in the study. "1" indicates that only one group was used, all other entries are taken from the study directly. Males and females were included separately only if the study specifically reported different results for each.
Lab_Wild - Whether the study species were reared in the lab/lab strains or taken from the wild. Species were considered wild if <2 generations were reared in the lab prior to the start of the study (e.g., if the study lab-acclimated the grandparental generation prior to creating the experimental parent generation, those were considered "wild")
*Taxonomy - The broad taxonomic group the study species belongs to. There were very few studies using plants so we collapsed perennial and annual plants into just "plants" (1_invertebrates, 2_vertebrates, 3_plants)
Stressor*from*paper - The stressor used in the experiments using the exact wording from the study
*Stressor_Category - Grouping stressors by more general categories (1_Temperature, 2_Chemistry, 3_Resource quality, 4_Species interaction, 5_Infection)
Stressor_type - Broadest category of stressor, either biotic or abiotic (1_Biotic, 2_Abiotic)
*Transmission_type - Which parent(s) were experimentally manipulated (1_Biparental, 2_maternal, 3_paternal)
Timing_P1 - The life stage when the parent early-life treatment/manipulation was administered (1_Embryo/Egg/Seed, 2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
Timing_P2 - The life stage when the parent later life treatment/manipulation was administered (2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
*Timing_O1 - The life stage when the offspring trait measure was taken (1_Embryo/Egg/Seed, 2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
*Devo_traits - The developmental mode of the study species, either direct development or biphasic development (1_Biphasic, 2_Direct)
Life_history_traits - The reproductive life history traits of the study species (1_Internal gestation, 2_External embryos, 3_External gametes, 4_clonal)
Mobility_Juvenile - The mobility of the juvenile phase of the organism (1_Sessile, 2_Mobile)
Mobility_Adult - The mobility of the adult phase of the organism (1_Sessile, 2_Mobile)
Trait*_*from_paper - The trait being measured in the offspring with the wording taken directly from the study
Trait_Category - Traits grouped by more general categories (e.g., Mass/Weight, Length/Size, Survival, Metabolism/respiration, etc.)
*Trait_Type - Traits grouped into six broad categories (1_Physiology, 2_Morphology, 3_Life_history, 4_Survival, 5_Reproductive, 6_Behavior)
Trait_Unit - The unit of measurement of the trait (e.g., mm, g, seconds, etc.)
Negative*_*fitness_Correlation - Whether or not the trait has a negative correlation with fitness (i.e., a lower value is actually better, for example development time or latency to feed). For these traits, we reversed their sign to better understand our results as adaptive/maladative. A "0" indicates no correction was applied, a "1" indicates that the sign was reversed.
*Continuous_correction_applied - Whether or not a continuous correction was applied. For some studies, the mean or error term was equal to zero which cannot be used correctly in our effect size calculations so a continuous correction of 0.5 was applied to all values in that pairwise comparison (see Methods). A "0" indicates that no correction was applied, a "1" indicates that a continuous correction was applied.
*P1_treatment - The treatment ("control" or "stress") of the parent during their early life stage
*P2_treatment - The treatment ("control" or "stress") of the parent during their later life stage
*O_treatment - The treatment ("control" or "stress") of the offspring during their trait measurement (e.g., "control" if lengths were measured in control conditions, "stress" if offspring were exposed to temperature stress and their tolerance measured as the trait of interest)
Treatment_combo - All three treatment moderators (P1_treatment _ P2_treatment _ O_treatment) combined into one term (for graphing purposes)
Parent_combo - The parent treatment moderators (P_treatment _ P2_treatment) combined into one term (for graphing purposes)
*A_n_control - Sample size of the control treatment
*B_n_stress - Sample size of the stress treatment
*A_avg_control - The mean trait value of the control treatment
*B_avg_stress - The mean trait value of the control treatment
*A_sd_control - The standard deviation around the mean trait value of the control treatment
*B_sd_stress - The standard deviation around the mean trait value of the control treatment
NOTES - Additional notes or comments
3. Missing data codes: Only the "Author_Keywords" and "NOTES" columns should have blank cells, blank cells indicate information not retrieved or no additional information necessary
4. Specialized formats or abbreviations used:
P = parent
O = offspring
Design_B_lnRR_Spp.csv
1. Number of variables: 55
2. Number of cases/rows: 392
Variable list (*denotes used or described in analyses presented in manuscript):
ID - A unique number given to each row.
*Species - The genus and species used in the study (Genus_species)
Source - Database where the study was found - Scopus, WoS (Web of Science), or Both (study found on both Scopus and Web of Science)
Record Number - A unique number given to each study prior to the first screening
*Study_ID - A unique number given only to studies used in the final analyses (studies that made it past the first and second screening), formatted as "S#"
*Effect_size_ID - A unique number given to each effect size calculated from studies included in the final analysis, formatted as "E#"
Authors - The authors of the study (full last name, first letter of first name only)
Authors_FullName - The authors of the study (full last name, full first name)
Title - Study title
Abstract - Study abstract
Journal - Journal where study was published
Year - Year study was published
Author_Keyword - Keywords provided by authors (empty cells indicate that keywords were not provided upon download from database)
DOI - The digital object identifier of the study
DOI_Link - The address with the digital object identifier that links to the article
Population - Indicates if multiple populations/strains/sexes/groups were used in the study. "1" indicates that only one group was used, all other entries are taken from the study directly. Males and females were included separately only if the study specifically reported different results for each.
Lab_Wild - Whether the study species were reared in the lab/lab strains or taken from the wild. Species were considered wild if <2 generations were reared in the lab prior to the start of the study (e.g., if the study lab-acclimated the grandparental generation prior to creating the experimental parent generation, those were considered "wild")
*Taxonomy - The broad taxonomic group the study species belongs to. There were very few studies using plants so we collapsed perennial and annual plants into just "plants" (1_invertebrates, 2_vertebrates, 3_plants)
Stressor*from*paper - The stressor used in the experiments using the exact wording from the study
*Stressor_Category - Grouping stressors by more general categories (1_Temperature, 2_Chemistry, 3_Resource quality, 4_Species interaction, 5_Infection)
Stressor_type - Broadest category of stressor, either biotic or abiotic (1_Biotic, 2_Abiotic)
*Transmission_type - Which parent(s) were experimentally manipulated (1_Biparental, 2_maternal, 3_paternal)
Timing_P1 - The life stage when the parent early-life treatment/manipulation was administered (1_Embryo/Egg/Seed, 2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
Timing_P2 - The life stage when the parent later life treatment/manipulation was administered (2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
*Timing_O1 - The life stage when the offspring trait measure was taken (1_Embryo/Egg/Seed, 2_Hatchling/Neonate/Germination/Larva, 3_Juvenile/Seedling, 4_Adult)
*Devo_traits - The developmental mode of the study species, either direct development or biphasic development (1_Biphasic, 2_Direct)
Life_history_traits - The reproductive life history traits of the study species (1_Internal gestation, 2_External embryos, 3_External gametes, 4_clonal)
Mobility_Juvenile - The mobility of the juvenile phase of the organism (1_Sessile, 2_Mobile)
Mobility_Adult - The mobility of the adult phase of the organism (1_Sessile, 2_Mobile)
Trait*_*from_paper - The trait being measured in the offspring with the wording taken directly from the study
Trait_Category - Traits grouped by more general categories (e.g., Mass/Weight, Length/Size, Survival, Metabolism/respiration, etc.)
*Trait_Type - Traits grouped into six broad categories (1_Physiology, 2_Morphology, 3_Life_history, 4_Survival, 5_Reproductive, 6_Behavior)
Trait_Unit - The unit of measurement of the trait (e.g., mm, g, seconds, etc.)
Negative*_*fitness_Correlation - Whether or not the trait has a negative correlation with fitness (i.e., a lower value is actually better, for example development time or latency to feed). For these traits, we reversed their sign to better understand our results as adaptive/maladative. A "0" indicates no correction was applied, a "1" indicates that the sign was reversed.
*Continuous_correction_applied - Whether or not a continuous correction was applied. For some studies, the mean or error term was equal to zero which cannot be used correctly in our effect size calculations so a continuous correction of 0.5 was applied to all values in that pairwise comparison (see Methods). A "0" indicates that no correction was applied, a "1" indicates that a continuous correction was applied.
*P1_treatment - The treatment ("control" or "stress") of the parent during their early life stage
*P2_treatment - The treatment ("control" or "stress") of the parent during their later life stage
*O_treatment - The treatment ("control" or "stress") of the offspring during their trait measurement (e.g., "control" if lengths were measured in control conditions, "stress" if offspring were exposed to temperature stress and their tolerance measured as the trait of interest)
Treatment_combo - All three treatment moderators (P1_treatment _ P2_treatment _ O_treatment) combined into one term (for graphing purposes)
Parent_combo - The parent treatment moderators (P_treatment _ P2_treatment) combined into one term (for graphing purposes)
*A_n_control - Sample size of the control treatment
*B_n_stress - Sample size of the stress treatment
*A_avg_control - The mean trait value of the control treatment
*B_avg_stress - The mean trait value of the control treatment
*A_sd_control - The standard deviation around the mean trait value of the control treatment
*B_sd_stress - The standard deviation around the mean trait value of the control treatment
NOTES - Additional notes or comments
*lnRR - Effect size calculated using a log response ratio with correction (see Equation 1 in Methods)
*lnRRV - Variance around the effect size, sampling variance (see Equation 2 in Methods)
*Precision - The inverse of the standard error (or 1/SQRT(lnRRV))
db - The database the* taxize* package used to assign taxonomic information to each species (all were ncbi).
phylum - Phylum of the study species.
class - Class of the study species.
order - Order of the study species.
family - Family of the study species.
3. Missing data codes: Only the "Author_Keywords" and "NOTES" columns should have blank cells, blank cells indicate information not retrieved or no additional information necessary
4. Specialized formats or abbreviations used:
P = parent
O = offspring
lnRR = effect size (using log response ratio)
lnRR = sampling variance
Code/software
Code
We collected the mean, sample size, and variance (error terms) associated with offspring traits across all treatment combinations to calculate effect sizes and multiple pieces of additional information to serve as contextual moderators. All analyses were conducted in R (version 4.4.2). Due to various sources of non-independence in our data, we ran multilevel meta-analytic models and meta-regressions using the package metafor and the rma.mv function (Kim et al., 2020). We ran models on our data from Design A and Design B separately.
Meta-analysis_Analysis_Design A_12.19.24.Rmd
Meta-analytic and meta-regression analyses for our Design A data.
Meta-analysis_Analysis_Design B_12.19.24.Rmd
Meta-analytic and meta-regression analyses for our Design B data.
MetaAnalysis_DesignA_FIGURES_12.19.24.Rmd
Code to create the main graphs and visualizations in the manuscript (one exception being the phylogenetic tree which was created as part of the code in Meta-analysis_Analysis_Design A_12.19.24.Rmd).
MetaAnalysis_DesignA_FIGURES_12.19.24.Rmd
Code to create the main graphs and visualizations in the manuscript (one exception being the phylogenetic tree which was created as part of the code in Meta-analysis_Analysis_Design B_12.19.24.Rmd).
custom_func.R
A function written by Nakagawa et al. (2023) to streamline certain functions within the analysis. We highly recommend their tutorial and found it to be an invaluable tool while working through our own analyses.
Shinichi Nakagawa, Yefeng Yang, Erin Macartney, Rebecca Spake, and Malgorzata Lagisz. Quantitative synthesis: a practical guide to meta-analysis, meta-regression, and publication bias tests for environmental sciences. Environmental Evidence, 2023
Recommended packages
metafor, rotl, ape, taxize, MuMIn, OrchaRd
Access information
Data was derived from the following sources:
Design A
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Design B
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Neylan, I. P., Swezey, D. S., Boles, S. E., Gross, J. A., Sih, A., & Stachowicz, J. J. (2024). Within- and transgenerational stress legacy effects of ocean acidification on red abalone (Haliotis rufescens) growth and survival. Glob. Chang. Biol., 30(1), e17048.
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Shama, L. N. S. (2015). Bet hedging in a warming ocean: predictability of maternal environment shapes offspring size variation in marine sticklebacks. Glob. Chang. Biol., 21(12), 4387–4400.
Spinks, R. K., Donelson, J. M., Bonzi Lucrezia C and Ravasi, T., & Munday, P. L. (2022). Parents exposed to warming produce offspring lower in weight and condition. Ecol. Evol., 12(7), e9044.
Tate, A. T., & Graham, A. L. (2015). Trans‐generational priming of resistance in wild flour beetles reflects the primed phenotypes of laboratory populations and is inhibited by co‐infection with a common parasite. Funct. Ecol., 29(8), 1059–1069.
Yadav, T., Omkar, & Mishra, G. (2023). Maternal cannibalistic preferences affect offspring preferences and development in Menochilus sexmaculatus Fabricius (Coleoptera: Coccinellidae): A transgenerational investigation. Ethology, 129(2), 107–115.
Yin, X. W., Zhao, N. X., Wang, B. H., & Li Wen Jie and Zhang, Z. N. (2015). Transgenerational and within-generational induction of defensive morphology in Brachionus calyciflorus (Rotifera): importance of maternal effect. Hydrobiologia, 742(1), 313–325.
Yu, X., Tang, R., Liu, T., & Qiu, B. (2023). Larval and/or adult exposure to intraguild predator Harmonia axyridis alters reproductive allocation decisions and offspring growth in Menochilus sexmaculatus. Insects, 14(6).
Zimmer, C., Larriva, M., Boogert, N. J., & Spencer, K. A. (2017). Transgenerational transmission of a stress-coping phenotype programmed by early-life stress in the Japanese quail. Sci. Rep., 7(1).
Methods
This dataset was collected from published research papers as part of a meta-analysis examining the effects of transgenerational and developmental plasticity on organism stress tolerance. Raw data was collected from published manuscripts that fit a pre-determined set of criteria from either 1) raw data provdided by authors in a repository or via personal communicatio, 2) data presented in tables, 3) data mined using the MetaDigitise package in R from figures. These raw data were then analyzed using a meta-analytic model and a series of meta-regression models to determine factors/moderators that significantly contributed to patterns in offspring trait measures. We used two designs and analyzed them separately. The aim for Design A was to determine if there were significant effects of parental treatment (transgenerational plasticity) and offpspring early-life treatment (developmental plasiticity) and their potential interactions on later offspring traits. The aim for Design B was to determine if the timing of parental exposure to stress (in early life or later in life) impacted transgenerational patterns.