Data and code for: Transgenerational pathogen effects: Maternal pathogen exposure reduces offspring fitness
Data files
Jun 10, 2025 version files 59.60 KB
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aves.csv
2.71 KB
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edata.csv
5.47 KB
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griddata.csv
489 B
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Main_EXP.csv
3.03 KB
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NeoSize.csv
3.88 KB
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ranges.csv
1.31 KB
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README.md
12.08 KB
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TGV_vs_Metsch.csv
1.49 KB
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TGVcodeAnalyses.R
7.88 KB
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TGVcodeFigures.R
8.88 KB
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TGVsupplementcode.R
11.48 KB
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wt.csv
895 B
Abstract
Pathogens can alter the phenotype not only of exposed hosts, but also of future generations. Transgenerational immune priming, where parental infection drives reduced susceptibility of her offspring, has been particularly well explored, but pathogens can also alter life history traits of offspring. Here, we examined the potential for transgenerational impacts of a microsporidian pathogen, Ordospora pajunii, by experimentally measuring the impact of maternal exposure on offspring fitness in the presence and absence of parasites, and then developing mathematical models that explored the population-level impacts of these transgenerational effects. We did not find evidence of transgenerational immune priming: offspring of exposed mothers became infected at high rates, similar to offspring of unexposed mothers, and the infection burden did not differ between these two groups. We also did not find any evidence of transgenerational tolerance, where daughters of exposed mothers have higher fitness after infection. Instead, we found evidence for negative transgenerational impacts of infection: uninfected offspring of exposed mothers had substantially greater early life mortality than uninfected offspring of unexposed mothers. Offspring of exposed mothers also had reduced growth rate, fewer clutches, and fewer offspring. We propose that these observations should be considered transgenerational virulence, where a pathogen reduces the fitness of the offspring of infected hosts. Our parameterized mathematical model allowed us to explore the impacts of transgenerational virulence at the population level. If transgenerational virulence manifests as decreased reproduction or increased mortality in offspring, as we saw in the empirical portion of our study, this reduces total host density, infection prevalence, and infected host density, which could have implications for both host conservation and spillover risk. We propose that transgenerational virulence might be common and is a concept worthy of further empirical and theoretical exploration.
Dataset DOI: 10.5061/dryad.vx0k6dk41
Description of the data and file structure
Data and code for ECY25-0256 - "Transgenerational pathogen effects: Maternal pathogen exposure reduces offspring fitness"
The Related Works contains a link to code for the theoretical portion of the study.
The uploaded files contain data and code for the empirical portion of the study.
Files and variables
File: aves.csv
Description: Used in the code that contains the analyses and generates the figures for the empirical portion of the supplement, which is in TGVsupplementcode.R
Variables
- MOMID: id# of animal producing the embryos
- tx: which maternal care treatment. A= embryos removed at stage 1 (destructively sampled) corresponding to group A in Section S1.2 of the Appendix; “removed” is group B, and “not removed” is group C in Section S1.2.
- momp: maternal parasite treatment. Control=none. Micg= O. pajunii exposure
- msize: length of mom at embryo removal (in micrometers)
- yolk: average length of yolk of embryos produced (in micrometers)
- yolkrange: difference of largest-smallest yolk length in clutch (in micrometers)
- size: average length of embryos produced (in micrometers)
- sizerange: difference of largest-smallest embryo size in clutch (in micrometers)
- y/s: ratio of yolk/size
- s/ms: ratio of size/msize
- yolkratio: same as y/s
- momratio: same as s/ms
File: edata.csv
Description: Used in the code that contains the analyses and generates the figures for the empirical portion of the supplement, which is in TGVsupplementcode.R
Variables
- ID: individual ID
- momp: parasite treatment for the mothers of the individuals in this experiment; MicG = O. pajunii
- TX: which maternal care treatment. A= embryos removed at stage 1 (destructively sampled) corresponding to group A in Section S1.2 of the Appendix; “removed” is group B, and “not removed” is group C in Section S1.2.
- size: length of the animal producing the embryos (in micrometers)
- embryos: number of embryos produced in the clutch
- size/e: the ‘size’ column divided by the ‘embryos’ column
- neonates: number of neonates produced
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difference: embryos – neonates; 0 means all of the embryos survived to become neonates, whereas a number greater than that means some or all of the embryos did not survive
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difcountrupt: the number of the embryos that did not survive that resulted from rupture
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Matpara: same as momp, but now using “O.pajunii” instead of MicG
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EmbryoCare: same as Tx
Info on missing data in edata.csv:
- missing data for columns G, H, and I for treatment a individuals due to destructive sampling when embryos; for animals 105 & 106, missing data in columns D, E, and F is due to death of individual prior to producing a clutch
- all other rows with missing data are due to death of individual prior to producing a clutch
File: griddata.csv
Description: Used in the main text. This file has the data on infection burden for animals exposed to and infected with MicG (O. pajunii) The code that contains the analyses in the main text is in TGVcodeAnalyses.R The code that generates the figures associated with the empirical portion of this study (that is, Figures 2 and 3) in the main text is in TGVcodeFigures.R
Variables
- ID#: unique identifier of the individual
- Clone: Daphnia genotype used; S clone (also known as Standard or STD clone)
- mpara: Maternal exposure treatment (None = control, MicG = Ordospora pajunii)
- sum: total number of grid squares that contained spore clusters across the experiment
- scoreperday: sum divided by total days the animal lived
- scoreperinfectedday: sum divided by total days during which infection was observed in this animal
File: Main_EXP.csv
Description: Used in the main text. The code that contains the analyses in the main text is in TGVcodeAnalyses.R The code that generates the figures associated with the empirical portion of this study (that is, Figures 2 and 3) in the main text is in TGVcodeFigures.R
Variables
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ID: unique identifier for each (daughter) individual
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Mom: Unique identifier for each individual that was part of a larger project
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MomParasite: Exposure treatment for the mother (MicG = Ordospora pajunii, None = control)
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MomStatus: Whether the mother was exposed to a parasite (MicG) or not); this is redundant with the prior column
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Parasite: Exposure treatment of the daughter generation (MicG = Ordospora pajunii, None = control)
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Clone: Daphnia genotype used; STD clone (also known as Standard or S clone)
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Inf: whether the individual was successfully infected; a “No” for an exposed animal means it was exposed but did not develop an infection
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Prev: 1 indicates that the animal became infected; 0 indicates that it was not infected; missing data indicates the animal died before it could be reliably diagnosed as infected
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Clutches: the number of clutches produced by the animal over its lifespan
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Sum: Total number of offspring produced in the first three clutches
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C1size: length in micrometers at first reproduction
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C1: Number of offspring in the first clutch
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C1day: Day on which the first clutch was produced
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C2: Number of offspring in the second clutch
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C2day: Day on which the second clutch was produced
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C3: Number of offspring in the third clutch
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C3day: Day on which the third clutch was produced
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Deathday: Day of experiment on which the animal died (also see explanation for next variable, ‘died’)
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died: Censoring status – 1 indicates that Daphnia died, 0 indicates that it was accidentally killed/lost; in the latter case, deathday value indicates the last day the animal was found alive
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edied: Early death status – 1 indicates that the Daphnia died early, i.e. within 20 days of birth, 0 indicates that the Daphnia lived over 20 days
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sedied: Super early death status – 1 indicates that the Daphnia died within 15 days of birth, 0 indicates that the Daphnia lived over 15 days
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note: gives additional information about an animal that was accidentally killed
Missing data info: missing data is due to animal dying prior to being able to measure that variable
File: NeoSize.csv
Description: Used in the main text. The code that contains the analyses in the main text is in TGVcodeAnalyses.R The code that generates the figures associated with the empirical portion of this study (that is, Figures 2 and 3) in the main text is in TGVcodeFigures.R
Variables
- MomID: unique identifier of the individual that produced the neonate
- Clone: Daphnia genotype used; S clone (also known as Standard or STD clone)
- Gmapara: The exposure treatment for the Maternal Generation; note the reference here is to a grandmother because we are now looking at the F2 neonates; None = control, O.pajunii = exposure to MicG (a.k.a. Ordospora pajunii)
- mpara: The exposure treatment for the Daughter Generation; note the reference here is to a mother because we are now looking at the F2 neonates; None = control, O.pajunii = exposure to MicG/Ordospora pajunii
- Size: length of the neonate in micrometers
File: ranges.csv
Description: Used in the code that contains the analyses and generates the figures for the empirical portion of the supplement, which is in TGVsupplementcode.R
Variables
- MOMID: id# of animal producing the embryos
- momp: maternal parasite treatment. Control=none. Micg= O. pajunii exposure
- msize: length of mom at embryo removal (in micrometers)
- yolk: average length of yolk of embryos produced (in micrometers)
- yolk range: difference of largest-smallest yolk length in clutch (in micrometers)
- size: average length of embryos produced (in micrometers)
- sizerange: difference of largest-smallest embryo size in clutch (in micrometers)
File: TGVcodeAnalyses.R
Description: The code that contains the analyses in the main text.
File: TGVcodeFigures.R
Description: The code that generates the figures associated with the empirical portion of this study (that is, Figures 2 and 3) in the main text.
File: TGVsupplementcode.R
Description: The code that contains the analyses and generates the figures for the empirical portion of the supplement.
File: wt.csv
Description: Used in the code that contains the analyses and generates the figures for the empirical portion of the supplement, which is in TGVsupplementcode.R
Variables
- matpara: maternal parasite exposure treatment
- boat: weight of the (empty) weigh boat used in milligrams
- number: number of embryos weighed
- totwt: total weight including the weigh boat and embryos in milligrams
- wt: weight of just the embryos (calculated by subtraction: totwt – boat = wt) in milligrams
- indave: average weight of each embryo (wt/number) in milligrams
File: TGV_vs_Metsch.csv
Description: Used in the main text. The code that contains the analyses in the main text is in TGVcodeAnalyses.R The code that generates the figures associated with the empirical portion of this study (that is, Figures 2 and 3) in the main text is in TGVcodeFigures.R
Variables
- ID: unique identifier for each (daughter) individual
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mid: unique identifier of mother that produced the individual
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mompath: Exposure treatment for the mother (MicG = Ordospora pajunii, None = control)
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mstatus: Whether the mother was exposed to a parasite (MicG) or not); this is redundant with the prior column
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para: Whether the daughter individual was exposed to a parasite; None = control, Metsch = Metschnikowia bicuspidata
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tgvormet: tgv = mom exposed to MicG, daughter not exposed to anything; met = mom not exposed to anything, daughter exposed to Metschnikowia
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INF: whether the daughter individual became infected; all but one of the Metschnikowia-exposed individuals became infected
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clone: Daphnia genotype used; STD clone (also known as Standard or S clone)
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size: length in micrometers at first reproduction
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C1: Number of offspring in the first clutch
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C1day: Day on which the first clutch was produced
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C2: Number of offspring in the second clutch
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C2day: Day on which the second clutch was produced
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C3: Number of offspring in the third clutch
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C3day: Day on which the third clutch was produced
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Deathday: Day of experiment on which the animal died (also see explanation for next variable, ‘died’)
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died: Censoring status – 1 indicates that Daphnia died, 0 indicates that it was accidentally killed/lost; in the latter case, deathday value indicates the last day the animal was found alive
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edied: Early death status – 1 indicates that the Daphnia died early, i.e. within 20 days of birth, 0 indicates that the Daphnia lived over 20 days
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notes: has information about one animal
Missing data info: missing data is due to animal dying prior to being able to measure that variable
Code/software
The code for the empirical portion of the study uses R (run in RStudio). These were run in R version 4.5.0. Four of the files are used for the analyses and figures in the main text. These are:
Main Exp.csv
TGV vs Metsch.csv
NeoSize.csv
griddata.csv
The code that contains the analyses in the main text is in TGVcodeAnalyses.R
The code that generates the figures associated with the empirical portion of this study (that is, Figures 2 and 3) in the main text is in TGVcodeFigures.R
Four of the files are used for the analyses and figures in the supplement. These are:
aves.csv
edata.csv
ranges.csv
wt.csv
The code that contains the analyses and generates the figures for the empirical portion of the supplement is in TGVsupplementcode.R
The code for the theoretical portion of the study runs in Matlab.
Access information
Other publicly accessible locations of the data:
