DOI: 10.5061/dryad.pnvx0k70d
title: Temporal variation in early-life conditions impacts on later-life levels of infection in sex specific ways. Associated data and code

description: Parasites are a fundamental component of wild animal populations, often
 inducing sub-lethal chronic effects that impact host fitness and
 demography. However, the factors determining variation in infection burden
 are often poorly understood in wild systems. Environmental conditions can
 determine exposure to infection and the resources required to respond, but
 exhibit strong temporal variation. As these are predicted to become more
 variable, understanding how they shape infection is key to predicting the
 impact of environmental change on host populations. Responses to infection
 are shaped in early life potentially leading to lagged effects of
 environmental variation on fitness. The extent to which these are mediated
 by resources and later-life conditions remains unclear and may vary
 between the sexes who often differ in exposure and resource requirements.
 Here, we examine how intra- and inter-annual differences in hatching and
 breeding conditions influence infection levels throughout life. 
 We utilise data from a long-term population study of European shags
 (Gulosus aristotelis) on the Isle of May, Scotland, in which there is
 substantial variation in the timing of breeding within and between years
 and nematode parasite burden can be measured in vivo using endoscopy. We
 used two data sets; the first containing information on parasite burden
 collected in chicks, matched with early life monitoring data, and the
 second containing adult parasite burden data matched with early life and
 current breeding conditions. Sex, age and the age of the bird at the time
 of parasite burden quantification were also present. For adults multiple
 measurements of parasite burden were taken across life in some
 individuals. We show that adult parasite burden, is influenced by seasonal
 and annual differences in current and early life conditions, but different
 patterns were observed in adult males and females. Burdens increased
 across the season in chicks and adult females but not in adult males.
 Instead, early life effects better explained burden in adult males with
 those hatching later and in productive years displaying lower burdens.
 This suggests that early life may shape behaviour or physiology, impacting
 subsequent infection. Our findings reveal complex temporal effects on
 parasitism in species breeding in fluctuating environments. Incorporating
 seasonal and sex specific responses to parasitism is crucial to
 understanding how predicted environmental shifts could impact disease
 dynamics.
description: # Temporal Early life effects on parasitism - European shag data sets and
 code Dataset DOI: [10.5061/dryad.pnvx0k70d](10.5061/dryad.pnvx0k70d) ##
 Description of the data and file structure This data was collected in
 order to investigate the impact of the timing of early life and current
 breeding on nematode parasite burden at different life stages of European
 shag. To do this we quantified nematode parasite burden in chick and adult
 European shags and monitored their early life and breeding conditions. For
 chicks parasite burden was measured in three years, whereas for adults
 this was carried out across eight years. Throughout the date format
 DD/MM/YYYY is used and NAs and #VALUE indicates cases where data was not
 available.  ### Files and variables #### File:
 Temporal_earlylife_effects_chickdata_EE.Submission.xlsx
 **Description:** European shag chick parasite burden and early life data
 set along with data dictionary. Also provided in .csv. ##### Variables |
 **Variable** | **Description (where necessary)** | |
 :------------------------- |
 :----------------------------------------------------------------------------------------------------------------- | | Year.of.Endoscopy | | | BirdID | Unique ID associated with each individual across their life time | | Sex | Male or female based on molecular sexing or sexual dimorphism in adulthood. Not available for all chicks. | | Treatment | In years in which experiments were performed, only control birds were used | | GroupedTrt | In years in which experiments were performed, only control birds were used, NA indicates no experiment was present | | Visibility | Indicates the quality of the visibility during endoscopy (score from 1-5, with the most visible) | | WormCount | Number of nematode worms counted during endoscopy (number of worms) | | Hatchyear  | | | Hatchdate | | | Scaled.relative.hatch.date | The hatch date of each chick scaled to the mean of the season in which in hatched (days) | | Average.breeding.success | The average annual productivity (average number of chicks fledged per incubated nest) | | hMedSeasonScaled | The population median breeding breeding date in the year that a chick hatched (days) | | hScaledDateAb | Absolute hatch date of the chick scaled to the 1st of January in the year of hatching (days) | | Scaled to | The first of January in the year in which the chick hatched | | Season.med | The median hatch date of the breeding season in which the chick hatched | | Date.of.Endoscopy | | | aAge | Age of chick at endoscopy (days) | #### File: Final_early_life_data_used_in_adult_models_final_EE.submission.xl.xlsx **Description:** European shag adult parasite burden, early life and current breeding conditions data set along with data dictionary. Also provided in .csv. ##### Variables | **Variable** | **Description** | | :---------------- | :------------------------------------------------------------------------------------------------- | | BirdID | Unique bird ID | | hBreedEventID | Breeding event ID in hatch year | | Sex | | | aBurden | Final burden used (number of worms) | | Dataextract | Who extracted data from database | | aBurOrignal | Burdens before update from videos (number of worms) | | aYear | Year of sampling | | aAvbreed | Average breeding success in year of sampling (average number of chicks fledged per incubated nest) | | aDate | Sampling date | | aBreeding.event | Breeding event ID in sampling year | | aJanFirst | First of January in sampling year | | aScaledDateAb | Sampling date scaled to Jan first | | aAge | Age at Sampling (years) | | achickhatchdate | Offspring hatch date | | achickhatchscaled | Offspring hatch date scaled to first of Jan | | aChickage | Chick age at sampling ( days) | | Chick.stage | Stage of chicks at sampling (egg, chick) | | hYear | Hatch year | | hAvgBreed | Average breeding success in year of hatching (chicks per year) | | hDate | Hatch date  | | hJanFirst | First of January in hatch year | | hScaledDateRel | Hatch date relative to the population mean in hatch year (days) | | hScaledDateAb | Absolute hatch date, scaled to the first of Jan (days) | #### File: Temporal_earlylife_effects._European_shags_Chick_Analysis.R **Description:** The analysis for the impact of early life variables on European shag chick parasite burden. #### File: Temporal_earlylife_effects._European_shags_Adult_Final_Analysis_supported_variables.R **Description:** The analysis for the impact of early life and current breeding variables on European shag adult parasite burden. This script contains the final models for the analysis, run with only the best supported variables.  #### File: Temporal_earlylife_effects._European_shags_Adult_Initial_Analysis.All.varaibles.R **Description:** The analysis for the impact of early life and current breeding variables on European shag adult parasite burden. This script includes initial exploratory models for all representations of the timing of early life and current breeding. ## Code/software R version 4.4.1, and RStudio 2024.04.2 are required to view this data and code. The R packages "dplyr", "ggplot2", "lme4", "readr", "effects", "AICcmodavg", are required to run the analysis code. Three files containing code are included with this data submission. One file contains the analysis for the impact of early life variables on chick parasite burden. The chick script contains both initial models run to explore the best representations of early life variables, and the final models run using the best supported early life variables. For adults, initial exploratory models for all representations of the timing of early life and current breeding, and final models run with only the best supported variables, are presented in two different scripts.