https://doi.org/10.5061/dryad.vhhmgqp21

Description of the data and file structure

Experimental data and the R code used for the analyses detailed in the methods section of Rodseth et al. "Pleiotropic effects of melanin pigmentation: haemoparasite infection intensity but not telomere length is associated with morph in black sparrowhawks" are provided. The dataset consists of haemoparasite infection intensity values, as determined by blood slide analysis and quantitative PCR (qPCR) analyses, as well as relative telomere length as determined by qPCR. There are four files in total:

File 1 - Experimental data generated during the project (Experimental data_Rodseth.xlsx)

This file contains the haemoparasite intensities as determined by microscopy analysis of blood slides (for the 68/89 birds where this assay was performed) and the quantitative PCR data for haemoparasite intensity and relative telomere length (for all 89 birds). The information contained in each sheet within the file is as follows:

Sheet 1 contains the haemoparasite intensity values derived from microscopy examination of blood slides expressed as number of cells infected by Haemoproteus or Leucocytozoon parasites per 10,000 erythrocytes.

Sheet 2 contains the telomere length qPCR results. Column A contains the qPCR plate ID, column B the sample ID, column C the quantification cycle (Cq) and column D the calculated concentration for each technical replicate (derived from the standard curve). Mean calculated concentration and coefficient of variation for each biological replicate are provided in columns G and H, respectively.

Sheet 3 contains the SFSR qPCR results. This is a single copy nuclear non-coding region and was used for normalisation of telomere and parasite intensity qPCR results. Column A contains the qPCR plate ID, column B the sample ID, column C the quantification cycle (Cq) and column D the calculated concentration for each technical replicate (derived from the standard curve). Mean calculated concentration and coefficient of variation for each biological replicate are provided in columns G and H, respectively.

Sheet 4 contains the relative telomere length values (telomere length calculated concentration/SFSR calculated concentration). Column A contains the sample ID, column B the mean telomere length calculated concentration, column C the mean SFSR calculated concentration, and column D the relative telomere length for each of the 89 birds. Sample IDs beginning with J are the juvenile blood samples that were available for 12/89 of the adult birds e.g. J1 is the juvenile blood sample for adult bird 1.

Sheet 5 contains the haemoparasite qPCR results. The standard curve used in this experiment was generated from a 595-bp fragment of the Plasmodium falciparum genome amplified by PCR. The relative infection intensity values provided in this file were generated by normalisation to SFSR calculated concentrations for each biological sample. Column A contains the sample ID, column B the quantification cycle (Cq) and column C the calculated concentration for each technical replicate (derived from the standard curve). Mean calculated concentration and coefficient of variation for each biological replicate are provided in columns F and G, respectively. Column H contains the mean calculated concentrations for SFSR for each sample, and column I the relative infection intensity values. NA = no amplification.

File 2 - Data file for use with the R code provided in "R code.txt" (Data1.csv)

This file contains the relative telomere and parasite intensity infection values for each sample as determined by qPCR, as well as infection intensity values determined by microscopy (where performed). Metadata for each bird used in the study is provided as follows: Sex (male or female), Tel: (Relative telomere length determined by qPCR), WC (whether the bird was caught in the Western Cape province or not - yes or no), ParM (haemoparasite infection intensity as measured by microscopy), ParQ (haemoparasite infection intensity as measured by qPCR), Morph (dark or light), Sample (sample ID), Parabin (whether a haemoparasite infection was detected (1) or not (0) by qPCR), Mdata (whether haemoparasite infection intensity data as determined by microscopy was available for that individual, 0 = no, 1 = yes), MorphN (numerical coding of morph, with dark = 1 and light = 0), Date (date bird sampled), Year (year bird sampled), Month (month bird sampled), MonthN (numerical coding of month sampled, with January = 1 to December = 12), ParQlog (natural logarithm of haemoparasite infection intensity as measured by qPCR), Mass (g), Wing = (wing chord length in mm), Tarsus (tarsus length in mm), Ring no (Unique ring ID number, if present), Prov (province in which the bird was captured: EC = Eastern Cape, GP = Gauteng, KZ = Kwa-Zulu Natal, MP = Mpumalanga, WC = Western Cape), Lat (latitude at which the bird was captured), Long (longitude at which the bird was captured, LatA (latitude at which the bird was captured - numerical value only, no N or S), LongA (longitude at which the bird was captured - numerical value only, no E or W), CI (condition index - added to the dataset in R), NoCI (individuals for which CI was not available, indicated by 1), Plate (qPCR run), Breeding (whether the individual was captured during peak breeding season (B) or not (NB)), ParYN (whether a haemoparasite infection was detected (Y) or not (N) by qPCR, Micro (numerical coding of whether microscopy haemoparasite infection intensity data was available (1) or not (0)). Please note that all blank cells in this file are deliberate.

File 3 - Metadata for recaptured birds for use with the R code provided in "R code.txt" (Recruits Data.csv)

This file contains metadata for the twelve birds that were recaptured as adults and thus two blood samples (nestling and adult) were available for qPCR analysis. The following information is provided: Morph (dark or light), Sex (male or female), Age (adult age at sampling), Attrition (nestling relative telomere length - adult relative telomere length), Sample ID, Adult or nestling (whether the relative telomere length reported in the next column is from the adult or nestling), T/S (relative telomere length determined by qPCR), MorphRep (this is repeated so that adult morph is noted for the adult and nestling - required for some analyses in R), Haemoparasite intensity (infection intensity determined by qPCR), Haemoparasite infection (whether a haemoparasite infection was detected (1) or not (0) by qPCR), Baseline T/S (Relative telomere length in nestling). Please note that all blank cells in this file are deliberate.

File 4 - R code used for statistical analyses (R code.txt)

This file contains all the R code necessary to repeat the analyses described in the paper using the "Data1.csv" and "Recruits Data.csv" data files provided.