Data and code from: Delayed post-juvenile moult in malaria-infected Eurasian blackcaps
Data files
Jan 09, 2025 version files 195.88 KB
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README.md
12.17 KB
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SYLATR_PJMJuv10_data.xlsx
62.52 KB
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SYLATR_PJMJuv10_TESTdata.csv
121.19 KB
Abstract
Parasites have their strongest impact on fitness when host defences deplete resources needed for other critical life-history stages, such as development, breeding or migration. Among birds, one greatly neglected stage that could be altered by parasites is post-juvenile moult (PJM), through which yearling juvenile birds replace their fast-generated, low-quality juvenile feathers with adult-like feathers after leaving the nest. The earlier the birds complete PJM, the earlier they will be prepared to withstand forthcoming challenges, such as adverse winter conditions or migration. We used data from 435 juvenile Eurasian blackcaps (Sylvia atricapilla) sampled during three years in 26 localities spanning the wide range of environmental conditions across Iberian Spain to test whether haemosporidian infections (presence and abundance in blood of parasites of the genera Haemoproteus, Plasmodium and Leucocytozoon) were related to the progress of PJM. Controlling for body condition, sex, year and date of capture, infected blackcaps (single-infected or co-infected) had lower moult scores indicative of delayed moult, especially when birds had Plasmodium infections or high intensities of Haemoproteus parasites. Our results broaden the range of fitness costs that haemosporidian parasites may have on birds, as delayed post-juvenile plumage acquisition can impact subsequent key life-history stages.
README: Data and code for: Delayed post-juvenile moult in malaria-infected Eurasian blackcaps
https://doi.org/10.5061/dryad.x0k6djhvw
Description of the data and file structure
Files contains all the data and code necessary to reproduce the results of the paper "Delayed post-juvenile moult in malaria-infected Eurasian blackcaps". The data were collected to test the relationship between haemosporidian infections and the progress of post-juvenile moult in Iberian blackcaps Sylvia atricapilla. The datasets uploaded in Dryad includes field data of blackcaps (progress of post-juvenile moult, morphology, body condition, date and locality of capture, etc.) and laboratory data of parasite infections (results of PCR for detection of the genera Plasmodium, Haemoproteus and Leucocytozoon and microscopy data of intensity of infection of these parasites in the blood of birds). Files uploaded in Zenodo includes the R code to reproduce the statistical analyses.
NOTE: All files (from Dryad and Zenodo) must be in the same folder for the R code to run correctly.
Files and variables
Description of variables in the RAW DATA file:
Filename = SYLATR_PJMJuv10_data.xlsx (sheet = "SYLATR_PJMJuv10_data")
Individual data related with morphology, infection and sampling information.
- Original.order = code indicating the original raw order of the database
- Sample = individual sample code
- Year = Year, codes "2008", "2009" and "2011"
- Date = Date of capture (Excel date format)
- Locality = Name of the sampling locality
- Sex_PCR = Sex of each individual, codes "Female" and "Male"
- P_INF_PCR = status of Plasmodium infection, codes "1" for infected and "0" for uninfected
- H_INF_PCR = status of Haemoproteus infection, codes "1" for infected and "0" for uninfected
- L_INF_PCR = status of Leucocytozoon infection, codes "1" for infected and "0" for uninfected
- N_Haemoproteus = Number of different Haemoproteus lineages identified
- N_Plasmodium = Number of different Plasmodium lineages identified
- N_Leucocytozoon = Number of different Leucocytozoon lineages identified
- N_par = total number of haemosporidian lineages
- Total_Paras = total number of infected erythrocytes by any haemosporidian parasite in 50000 erythrocytes
- Total_H = number of infected erythrocytes by Haemoproteus parasites in 50000 erythrocytes
- Total_P = number of infected erythrocytes by Plasmodium parasites in 50000 erythrocytes
- Total_L = number of infected erythrocytes by Leucocytozoon parasites in 50000 erythrocytes
- N_Gen = number of haemosporidian genera (Haemoproteus, Plasmodium or Leucocytozoon)
- PJM_score = Post-juvenile moult score using a Swedish code that ranges from 0 (when primary feathers are still growing) to 6 (post-juvenile moult completed, this category was never observed). Codes "0","1","2","3","4" and "5"
- OBS = Person taking post-juvenile moult scores to each bird. Codes are IDH = Iván de la Hera, and JPT = Javier Pérez-Tris
- BodyMass = body mass (g)
- Tarsus = tarsus length (mm)
- Longitude = longitude of locality coordinates
- Latitude = latitude of locality coordinates
- HourRaw = time of capture (hh:mm:ss)
Description of variables in the DATA file prepared for analysis:
Filename = SYLATR_PJMJuv10_TESTdata.csv
Individual data related with morphology, infection and sampling information including variables in a format suitable for statistical analyses.
- Original.order = code indicating the original raw order of the database
- Sample = individual sample code
- Year = Year, codes "2008", "2009" and "2011"
- Date = Date of capture (Excel date format)
- Locality = Name of the sampling locality
- Sex_PCR = Sex of each individual, codes "Female" and "Male"
- P_INF_PCR = status of Plasmodium infection determined by PCR, codes "1" for infected and "0" for uninfected
- H_INF_PCR = status of Haemoproteus infection determined by PCR, codes "1" for infected and "0" for uninfected
- L_INF_PCR = status of Leucocytozoon infection determined by PCR, codes "1" for infected and "0" for uninfected
- N_Haemoproteus = Number of different Haemoproteus lineages identified
- N_Plasmodium = Number of different Plasmodium lineages identified
- N_Leucocytozoon = Number of different Leucocytozoon lineages identified
- N_par = total number of haemosporidian lineages
- Total_Paras = total number of infected erythrocytes by any haemosporidian parasite in 50000 erythrocytes
- Total_H = number of infected erythrocytes by Haemoproteus parasites in 50000 erythrocytes
- Total_P = number of infected erythrocytes by Plasmodium parasites in 50000 erythrocytes
- Total_L = number of infected erythrocytes by Leucocytozoon parasites in 50000 erythrocytes
- N_Gen = number of haemosporidian genera (Haemoproteus, Plasmodium or Leucocytozoon)
- PJM_score = Post-juvenile moult score using a Swedish code that ranges from 0 (when primary feathers are still growing) to 6 (post-juvenile moult completed, this category was never observed). Codes "0","1","2","3","4" and "5"
- OBS = Person taking post-juvenile moult scores to each bird. Codes are IDH = Iván de la Hera, and JPT = Javier Pérez-Tris
- BodyMass = body mass (g)
- Tarsus = tarsus length (mm)
- Longitude = longitude of locality coordinates
- Latitude = latitude of locality coordinates
- HourRaw = time of capture (hh:mm:ss)
- INF_BIN_PCR = binary infection status by PCR, codes "1" for infected and "0" for uninfected
- INF_BIN_PCRSm = binary infection status determined by PCR together with smears microscopy revision, codes "1" for infected and "0" for uninfected
- H_INF_PCRSm = status of Haemoproteus infection determined by PCR together with smears microscopy revision, codes "1" for infected and "0" for uninfected
- P_INF_PCRSm = status of Plasmodium infection determined by PCR together with smears microscopy revision, codes "1" for infected and "0" for uninfected
- L_INF_PCRSm = status of Leucocytozoon infection determined by PCR together with smears microscopy revision, codes "1" for infected and "0" for uninfected
- INF_MULT_PCR = multiple status of infection determined by PCR, codes "uninfected", "singleinfected" and "coinfected"
- INF_MULT_PCRSm = multiple status of infection determined by PCR together with smears microscopy revision, codes "uninfected", "singleinfected" and "coinfected". "NA" is used for missing data
- INF_MULT_PCRSmf = variable INF_MULT_PCRSm in factor format
- PJM_score_num = variable PJM_score in numeric format
- Sex_PCR_f = variable Sex_PCR in factor format
- Year_f = variable year in factor format
- jul_date = date of capture in Julian date, which is the number of days since January 1 each year
- P_INF_PCRf = variable P_INF_PCR in factor format
- H_INF_PCRf = variable H_INF_PCR in factor format
- L_INF_PCRf = variable L_INF_PCR in factor format
- Total_H_log = log10 of (Total_H +1)
- Total_P_log = log10 of (Total_P + 1)
- Total_L_log = log10 of (Total_L + 1)
- Hour = hour in HourRaw
- Minute = minutes in HourRaw
- Time_sec = time in seconds format of HourRaw variable
- Time_bin = time of capture as a dichotomous factor with codes "MORNING" and "AFTERNOON"
- BCjuv = body condition of juvenile blackcaps
References:
Bensch S, Lindström A. 1992 The age of young Willow Warblers Phylloscopus trochilus estimated from different stages of post-juvenile moult. Ornis Svec. 2, 23–28.
Code/software
R software is required to run the analysis code. The analyses were run with R version 4.2.3.
R studio is required to run the quarto files.
All R packages used in the analyses are mentioned in the corresponding scripts.
In Zenodo repository you can find the following files to run the analyses with the above data:
Readme file:
README file Spain_SYAT_PJM Rcode.txt It contains information to help run the analysis correctly (workflow as described here).
Description of R SCRIPT files:
- Filename =
Spain_SYAT_PJM_db.qmd..... data formatting and description previous to analysis. As a result, the "SYLATR_PJMJuv10_TESTdata.csv" file is generated, which is the database prepared for analysis. - Filename =
Spain_SYAT_PJM_brms_test1.qmd.....for analyses including all PJM data. - Filename =
Spain_SYAT_PJM_brms_test2.qmd.....for analyses with the subset PJM data excluding PJM scores with very low frequencies (0 and 5). - Filename =
Spain_SYAT_PJM_brms_test3.qmd.....for analyses testing the covariate (body condition and Julian date) correlations with haemosporidian infection variables.
Description of files in the Results_RDS folder
Each final statistical model is saved as an RDS file in the folder "Results_RDS" to allow accessing results without running the whole code. If you want to open these files with the above R scripts you have to move the files to the same directory as the R scripts.
RDS files with results from Spain_SYAT_PJM_brms_test1.qmd:
SYLATR_MULT.brm.ord.rds.....Test including multiple status of infectionSYLATR_MULT.brm.ord.RELEVEL.rds.....Test including multiple status of infection. RELEVEL Multiple status of infection factor for comparison of multiple and single infected levels with uninfected levelALLParload_brm.rds.....Test including total parasite loadSYLATR_PLAS_brm.rds.....Test including Plasmodium status of infectionPlas_Ploadbin_brm_ord.rds.....Test including Plasmodium parasite loadSYLATR_HAEM_brm.ord.rds.....Test including Haemoproteus status of infectionHaem_Hload_brm.rds.....Test including Haemoproteus parasite loadSYLATR_LEUCO_brm.rds.....Test including Leucocytozoon status of infectionLeuco_Lload_brmbin.rds.....Test including Leucocytozoon parasite load
RDS files with results from Spain_SYAT_PJM_brms_test2.qmd:
SYLATR_MULT.brm.ordRED.rds.....Test including multiple status of infectionSYLATR_MULT.brm.ordRED.RELEVEL.rds.....Test including multiple status of infection. RELEVEL Multiple status of infection factor for comparison of multiple and single infected levels with uninfected levelALLParload_brmRED.rds.....Test including total parasite loadSYLATR_PLAS_brmRED.rds.....Test including Plasmodium status of infectionPlas_Ploadbin_brm_ordRED.rds.....Test including Plasmodium parasite loadSYLATR_HAEM_brm.ordRED.rds.....Test including Haemoproteus status of infectionHaem_Hload_brmRED.rds.....Test including Haemoproteus parasite loadSYLATR_LEUCO_brmRED.rds.....Test including Leucocytozoon status of infectionLeuco_Lload_brmbinRED.rds.....Test including Leucocytozoon parasite load
RDS files with results from Spain_SYAT_PJM_brms_test3.qmd:
ESMC_SYLATR_MULTdep.brm.rds.....Test including multiple status of infection as dependent variableESMC_SYLATR_MULTdep.brmref.rds.....Test including multiple status of infection as dependent variable.RELEVEL Multiple status of infection factor for comparison of multiple and single infected levels with uninfected levelESMC_SYLATR_ParLoaddep.brm.hlog.rds.....Test including total parasite load as dependent variableESMC_SYLATR_PLASdep.brm.rds.....Test including Plasmodium status of infection as dependent variableESMC_SYLATR_Ploaddep.brm.rds.....Test including Plasmodium parasite load as dependent variableESMC_SYLATR_HAEMdep.brm.rds.....Test including Haemoproteus status of infection as dependent variableESMC_SYLATR_HLoaddep.brm.hlog.rds.....Test including Haemoproteus parasite load as dependent variable (family= hurdle_lognormal)ESMC_SYLATR_Hloaddep.brm.hnegb.rds.....Test including Haemoproteus parasite load as dependent variable (family= hurdle_negbinomial)ESMC_SYLATR_LEUCOdep.brm.rds.....Test including Leucocytozoon status of infection as dependent variableESMC_SYLATR_Lloaddep.brm.rds.....Test including Leucocytozoon parasite load as dependent variable
Access information
Other publicly accessible locations of the data:
- None.
Data was derived from the following sources:
- Collected by authors.
Methods
The methods are detailed in the associated article.