Avian eggshell wettability by Attard et al. 2021

The data and R scripts used in Attard et al. 2021 "Ecological drivers of eggshell wettability in birds" published in Journal of The Royal Society Interface are divided into two compressed folders. Description of each folder and the files contained are provided below.<br><b><br></b><b>FOLDER 1: EGGSHELL WETTABILITY RAW DATA AND R SCRIPT TO PROCESS DATA</b>This folder contains all the raw excel files for contact angle over time across 441 bird species as well as the R script (1_Rmarkdown_Extract_wettability_data.Rmd) used to combine and process these data to obtain specimen specific wettability measures and species averages. Influential values were removed based on cook's distance. The water droplet contact angle were extracted at specific time points to obtain two response variables: initial contact angle and spreadability, as described in the manuscript.<b><br></b>Contact angles were recorded every ~0.5 seconds starting from the point that the water droplet (9 uL) made contact with the eggshell surface to ~25 seconds later. Each excel file is a separate test. Each eggshell was prepared by gently cleaning the outer surface with damp cotton buds to remove dirt on the surface. <br>Previously blown whole eggshells of 441 bird species were obtained from the class II collection at the Natural History Museum, Tring (NHM, UK) and destructive eggshell collection at the Western Foundation of Vertebrate Zoology, Camarillo (WFVZ, USA), which are intended for scientific research. For NHM eggs, each clutch is distinguished by their registration year, batch and partcode, and each egg was given a unique ID number within each species. <br>In the R script, any specimens with influential values based on cook's distance were excluded from the database. The script then creates two csv files for eggshell wettability mean values per specimen and per species. These were used for MCMCglmm, PGLS and creation of figures (see Folder 2).<b><br></b><b>Species eggshell conductance phylogeny files:</b>The nexus (nex) tree file (Hackett_phylogenetic_tree.nex) contains avian phylogenetic trees constructed online (http://www.birdtree.org) using the primary backbone tree of Hackett <i>et al</i>. 2008. Ten thousand trees were constructed, and comprise of all species included in this study.<br><b>Life-history data and sources:</b> The excel file (lifehistory_data.xlsx) contains all life-history traits for each species investigated. Sources for life-history traits are included in the main tab and second tab within the excel file. <br><br><b>FOLDER 2: SPECIMEN AND SPECIES WETTABILITY AND PHYLOGENETIC ANALYSIS</b>The species_eggshell_wettability_data.csv file is used to run R markdown scripts for phylogenetic comparative analysis and create phylogenetic tree diagrams and figures.<br><b>Species eggshell conductance phylogeny file:</b>The newick (nwk) tree file (wettability_phylogenetic_tree.nwk) is the maximum clade credibility tree generated from the "1_Rmarkdown_Extract wettability data" script in Folder 1. This tree is used for phylogenetic comparative analysis and to create the phylogenetic tree diagrams in the paper.<br><br><b>R script for phylogenetic comparative analysis: </b>The "2_R Markdown_Phylogenetic_Comparative_Analysis.Rmd" file measures phylogenetic signal and runs PGLS and MCMCglmm models for eggshell wettability across all birds. It also creates figures that assess collinearity. A subset of this data was used to run the same analyses for passerines and non-passerines separately in a different script based on this one.<br><br><b>R script for phylogenetic tree diagrams and figures: </b>The "3_RMarkdown_Figures.Rmd" file creates phylogenetic tree diagrams, hybrid boxplots and scatterplots included in this paper.<br><b><br></b><b>R script for repeatability test: </b>The "4_RMarkdown_repeatability_ANOVA_pairedttest" script performs repeatability tests for eggshell wettability measured at two locations on the same fragment across multiple eggs. Data used is "shell_fragment_wettability_data.csv".<b><br></b><br>