DOI: 10.5061/dryad.vx0k6dk41
title: Data and code for: Transgenerational pathogen effects: Maternal pathogen exposure reduces offspring fitness

description: 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.
description: # Transgenerational pathogen effects: Maternal pathogen exposure reduces
 offspring fitness Dataset DOI:
 [10.5061/dryad.vx0k6dk41](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 * 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 * difcountrupt: the number of the embryos that did
 not survive that resulted from rupture * Matpara: same as momp, but now
 using “O.pajunii” instead of MicG * 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 * ID: unique identifier for each (daughter) individual *
 Mom: Unique identifier for each individual that was part of a larger
 project * MomParasite: Exposure treatment for the mother (MicG = Ordospora
 pajunii, None = control) * MomStatus: Whether the mother was exposed to a
 parasite (MicG) or not); this is redundant with the prior column *
 Parasite: Exposure treatment of the daughter generation (MicG = Ordospora
 pajunii, None = control) * Clone: Daphnia genotype used; STD clone (also
 known as Standard or S clone) * Inf: whether the individual was
 successfully infected; a “No” for an exposed animal means it was exposed
 but did not develop an infection * 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 * Clutches: the number of clutches produced by the animal over
 its lifespan * Sum: Total number of offspring produced in the first three
 clutches * C1size: length in micrometers at first reproduction * C1:
 Number of offspring in the first clutch * C1day: Day on which the first
 clutch was produced * C2: Number of offspring in the second clutch *
 C2day: Day on which the second clutch was produced * C3: Number of
 offspring in the third clutch * C3day: Day on which the third clutch was
 produced * Deathday: Day of experiment on which the animal died (also see
 explanation for next variable, ‘died’) * 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 * 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 * 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 * 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 -
 mid: unique identifier of mother that produced the individual - mompath:
 Exposure treatment for the mother (MicG = Ordospora pajunii, None =
 control) - mstatus: Whether the mother was exposed to a parasite (MicG) or
 not); this is redundant with the prior column - para: Whether the daughter
 individual was exposed to a parasite; None = control, Metsch =
 Metschnikowia bicuspidata - tgvormet: tgv = mom exposed to MicG, daughter
 not exposed to anything; met = mom not exposed to anything, daughter
 exposed to Metschnikowia - INF: whether the daughter individual became
 infected; all but one of the Metschnikowia-exposed individuals became
 infected - clone: Daphnia genotype used; STD clone (also known as Standard
 or S clone) - size: length in micrometers at first reproduction - C1:
 Number of offspring in the first clutch - C1day: Day on which the first
 clutch was produced - C2: Number of offspring in the second clutch -
 C2day: Day on which the second clutch was produced - C3: Number of
 offspring in the third clutch - C3day: Day on which the third clutch was
 produced - Deathday: Day of experiment on which the animal died (also see
 explanation for next variable, ‘died’) - 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 - 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 - 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: *
 [https://github.com/kmmcintire/TGV/tree/main](https://github.com/kmmcintire/TGV/tree/main)