DOI: 10.5061/dryad.4f4qrfjnh
title: Data from: Disease resistance is more costly at younger ages: An explanation for the maintenance of juvenile susceptibility

description: High juvenile susceptibility drives infectious disease epidemics across
 kingdoms, yet the evolutionary mechanisms that maintain this
 susceptibility are unclear. We tested the hypothesis that juvenile
 susceptibility is maintained by high costs of juvenile resistance by
 quantifying the genetic correlation between host fitness and age-specific
 innate resistance to a fungal pathogen in a wild plant. We found
 significant fitness costs associated with disease resistance at juvenile
 but not at adult host stages, and show that the magnitude of these
 juvenile resistance costs are sufficient to prevent the spread of juvenile
 resistance in models. Our results provide the first direct evidence that
 costs of resistance decrease with host age, and provide an explanation for
 the maintenance of epidemiologically important juvenile susceptibility in
 natural populations.
description: Two data sets are included: 
 Results from greenhouse inoculation studies on 45-full S.
 latifolia plants at 4 ages (9, 19, 78, and 104 days)
 Measurements of survival, flowering, and fruiting over 2 years
 for 721 plants from the same full sib families planted in a common garden
 in Beltsville, MD We include both the raw
 data, and a combined data set with both the resitance measures and
 survival and flowering field data.   Scripts for the
 analsyis are also included. These are descripted in the
 manuscript. 
description: # Disease resistance is more costly at younger ages: An explanation for
 the maintenance of juvenile susceptibility
 [https://doi.org/10.5061/dryad.4f4qrfjnh](https://doi.org/10.5061/dryad.4f4qrfjnh) ## Description of the data and file structure ### Files and variables #### File: data.zip **Description:** Four files are included. Three raw data files, and one summary data file for analysis: **resistance.csv** – Family level resistance data at each of four ages from greenhouse experiments.  o   **family**- name of full sib plant family (character variable: some are numbers, others a combination of numbers and letters e.g. ‘IB6’) o   **n.9d** – number of plants that were inoculated by the low-dose 3uL drop inoculation method at 9 days.  For this, and n.19d, n.78d, and n.104d: Only plants that ultimately flowered and could be scored for the presence or absence of disease are included in this total. NA indicates no data for that family at that age. o   **n.19d** – number of plants that were inoculated by the low-dose 3uL drop inoculation method at 19 days. o   **n.78d** – number of plants that were inoculated by the high-dose spray-inoculation method at 78 days. This only includes the number plants that were in reproductive stage (e.g. flowering or bolting) at the time of inoculation. o   **n.104d** – number of plants that were inoculated by the high-dose spray-inoculation method at 104 days. This only includes the number plants that were in reproductive stage (e.g. flowering or bolting) at the time of inoculation. o   **prop.healthy.9d** – the proportion of plants inoculated at 9 days that flowered healthy. o   **prop.healthy.19d** – the proportion of plants inoculated at 19 days that flowered healthy. o   **prop.healthy.78d** – the proportion of plants inoculated at 78 days that flowered healthy (high inoculation dose treatment). o   **prop.healthy.104d** – the proportion of plants inoculated at 104 days that flowered healthy (high inoculation dose treatment). o   **n78d.ld** - number of scored plants that were inoculated at 78 days by the low-dose 3uL drop inoculation method.   o   **n104d.ld** - number of scored plants that were inoculated at 104 days by the low-dose 3uL drop inoculation method.   o   **prop.healthy.78d.ld –** the proportion of plants inoculated at 78 days that flowered healthy (low inoculation dose treatment). o   **prop.healthy.104d.ld –** the proportion of plants inoculated at 104 days that flowered healthy (low inoculation dose treatment). **field.y1.csv** – Complete year 1 (2020) field data – survival, flowering and fruit for each individual plant in the field by date in the field in year 1 o   **col.colpos** - column and position in field o   **family** - full sib plant family o   **column** - column in field (1-14) o   **position.in.columns** - Position down column (1-53) o   **sex.consensus** - Sex of plant in field (F= female, M= male).  If a plant died before flowering its sex is listed as 'X' o   **Columns 6-16: ‘abs.flwr.[date]’** – 10 columns listing the actual flower counts for 10 observation periods spanning july to Dec 2020.  The data for each observation period is listed in column heading. All dates are recorded at month.day.year, with month as the abbreviated 3 letter english month.   o   Columns 17-27:**‘ord.flwr.[date]’** – Absolute flower counts per date (columns 6-16 above) converted into the ordinal scale of flower counts adopted in 2021. [0=0,1=1-10, 2=11-50, 3=51-200, 4&gt;200, see paper for details and justification]. o   Columns 28-49: **‘abs.fruit.[date]’** –columns listing the actual fruit counts for observation periods spanning july to Dec 2020.  The data for each observation period is listed in column heading.  o   Columns 50-71: **‘ord.fruit.[date]**’ – Conversion of absolute fruit number into ordinal scale o   Columns 72-97:**‘status [date]’** –Categorical status of plant at each date: X = dead, V= vegetative, B = bolting (sending up flowering stalk but not yet flowering), M= flowering (male), F= flowering (female), FL= flowering, FR = in fruit (but no open flowers), NA= missing data. o   **alive.dec.03.2020** = binomial marker whether the plant was still visibly alive in Dec 2020. **field.y2.csv** – Complete year 2 (2021) field data– survival, flowering and fruit for each individual plant in the field by date in the field in year 2 o   **col.colpos** - column and position in field o   **family** - full sib plant family o   **column** - column in field (1-14) o   **position.in.columns** - Position down column (1-53) o   **Sex** - Sex of plant in field (F= female, M= male).  If a plant died before flowering its sex is listed as 'X’ General description of data columns: Columns have a prefix and then a date in 2021 when the data was collected.  Below the prefix is described o   **status.[date]** - Categorical status of plant at each date: X = dead, V= vegetative, B = bolting (sending up flowering stalk but not yet flowering), M= flowering (male), F= flowering (female), FL= flowering, FR = in fruit (but no open flowers), NA= missing data. o   **flwr.[date]** – Ordinal flower score for that date.  [0=0,1=1-10, 2=11-50, 3=51-200, 4&gt;200, see paper for details and justification]. Plants marked with ‘NA’ were marked dead (see status). o   **dis.flwr.[date]** – Ordinal number of infected flowers (if any).   Disease was introduced late into the second year (see methods). o  **Notes.[date]** – Record of any field notes entered for that date. **merged.by.plant.csv** – Family level resistance data merged with summary statistics of field data o   **column** – column in field (1-14) o   **position.in.columns** – position along column in field (1-53) o   **col.colpos** - column and position in field o   **family** - full sib plant family o   **sex** – Sex of plant in field (F= female, M= male).  If a plant died before flowering its sex is listed as 'X’ o   **surv.yr1** – a binomial variable: 1 = survived to the beginning of the first flowering period of yr1, 0 = died before the beginning of the first flowering period of yr1 o   **surv.yr2** - a binomial variable: 1 = survived to the beginning of the first flowering period of yr2, 0 = died before the beginning of the first flowering period of yr2 o   **rep.yr1** – a binomial variable: 1=reproduced at least 1 flower during yr1, 0   =  no flowers during yr1) o   **rep.yr2** - a binomial variable: 1=produced at least 1 flower during yr2, 0   =  no flowers during yr2) o   **ord.flwr.sum.yr1** – sum of all the ordinal flower scores for yr1 o   **ord.flwr.sum.yr2** – sum of all the ordinal flower scores for yr2 o   **fruit.yr1 -** a binomial variable: 1=produced at least 1 fruit during yr1, 0=no fruit in yr1) o   **fruit.yr2** - a binomial variable: 1=produced at least 1 fruit during yr2, 0=no fruit in yr2) o   **ord.fruit.sum.yr1**-– sum of all the ordinal fruit scores for yr1 o   **ord.fruit.sum.yr2**-– sum of all the ordinal fruit scores for yr2 o   **prop.healthy.9d** – family-level resistance score (proportion healthy) from greenhouse inoculation test at 9 days (low dose inoculation treatment) o   **prop.healthy.19d** family-level resistance score (proportion healthy) from greenhouse inoculation test at 19 days (low dose inoculation treatment) o   **prop.healthy.78d** - family-level resistance score (proportion healthy) from greenhouse inoculation test at 78 days (high dose inoculation treatment) o   **prop.healthy.104d**- family-level resistance score (proportion healthy) from greenhouse inoculation test at 104 days (high dose inoculation treatment) o   **prop.healthy.78d.ld** - family-level resistance score (proportion healthy) from greenhouse inoculation test at 78 days (low dose inoculation treatment) o   **prop.healthy.104d.ld** - family-level resistance score (proportion healthy) from greenhouse inoculation test at 104 days (low dose inoculation treatment) o   **alive.dec.03.2020** – binomial variable; 1= alive, 0 = dead o   **alive.nov.04.2021**– binomial variable; 1= alive, 0 = dead ## Code/software **R-scripts** 8 script files are included that cover all data analysis presented in the paper and supplemental materials.   Non-aster analyses: * **analyze.merged.R** – All of the non-aster analyses including 1) pairwise comparisons of resistance scores across families (Fig 1) and 2) regressions between age-specific resistance scores and individual fitness components (Fig 3). * **field.analysis.flwr.R** – Make Figure 2 E and F (date versus mean flower score by sex) * **field.analysis.fruit.R** – Make Figure S1 A and B (date versus mean fruit score) * **Fig S4 Yr1 fitness.R** – Code for generating Figure S4 – (need to run ‘analyze.merged.R’ first).  This has the same formatting as the Fig S4 in the manuscript.  * **Fig S5 Yr1 fitness.R** – Code for generating Figure S5 – (need to run ‘analyze.merged.R’ first) Aster analyses: *  **asterFunctions.R** – Functions used to run aster analyses and make aster graphs *  **asteranalysis.R** – Aster models that test whether resistance at each age predict fitness in the field, calculate fitness of most and least resistant genotype, assess affect of family on fitness * **aster.full.R** – Aster models that compare a “full” model that includes sex and resistance at every age as predictors with subset models that only include resistance scores at some ages. This analysis only includes families with resistance scores at every age Evolutionary invasion model: * **Complete invasion model.R** - Code for running the SI model to determine the effect of cost of resistance on the evolutionary invasion of juvenile resistance. * **Sensitivity analysis.R** - SI model where all parameters are drawn from distributions.