Avian eggshell conductance by Attard and Portugal 2021

The data and R scripts used in our paper "Climate variability and parent nesting strategies influence gas exchange across avian eggshells" are divided into three compressed folders. Description of each folder and the files contained are provided below.<b><br></b><b>FOLDER 1: EGGSHELL CONDUCTANCE DATA</b><b><br></b><b>Specimen eggshell conductance data from laboratory database file: </b>This data contains water vapour conductance of whole eggs, using the standard protocol of measuring the decrease in mass through water loss over consecutive days, in eggs kept in constant moisture-free conditions. Each eggshell was prepared by gently cleaning the outer surface with damp cotton buds to remove dirt on the surface. The egg was then filled with distilled water through the blow hole using a plastic syringe. Once filled to capacity, the blow hole was dried then sealed then placed in an acrylic desiccator cabinet at 30±1°C. Self-indicating silica gel were placed in the bottom tray of the desiccator to remove all moisture so that any loss in mass in the eggs was entirely due to the diffusion of water vapour via the shell pores from inside the egg to the ambient air. The first 24-hours can give unexpectedly high mass loss values as the outer surface of the shell also dries out. Therefore, the eggs were left 24-hr before being weighed to the nearest 0.1 mg, before being returned to the desiccators. Eggs were weighed at the same time of day on three successive days to give two values of 24-hr mass loss (M_H2O). These two values were averaged for specimen-specific M_H2O. Calculation of water vapour conductance of the shell was conducted as previously described. ). The water vapour pressure difference across the eggshell was equal to the saturation pressure at 30^oC (31.84 torr) as the osmotic pressure of the albumen does not depress the vapour pressure within the shell, and the water pressure in the desiccator is zero.<br>Previously blown whole eggshells of 182 bird species were obtained from the class II collection at the Natural History Museum, Tring (NHM, UK), which are intended for scientific research. Each clutch is distinguished by their registration year, batch and partcode, and each egg was given a unique ID number within each species. Any eggs with &gt;30% difference in water loss between each 24-hr period or were considered influential based on cook's distance were excluded from the database.<b><br></b><b>Species eggshell conductance from laboratory and literature and life-history traits database files: </b>Water vapour conductance (<i>G</i>_H2O) of whole eggs was established using the standard protocol of measuring the decrease in mass through water loss over consecutive days, in eggs kept in constant moisture-free conditions. Previously blown whole eggshells of 182 bird species were obtained from the class II collection at the Natural History Museum, Tring (NHM, UK). Mean<i> G</i>_H2O values of whole eggs reported in the literature were also incorporated if specimens had been measured under constant conditions (temperature and humidity), and followed standard protocols.<br>The excel file (species_eggshell_conductance_data_references.xlsx) contains eggshell conductance and life-history traits for each species investigated. Primary and secondary sources for conductance values and sources for life-history traits are included in the main tab and separate tabs within the excel file. The first tab in this spreadsheet was saved as a csv file (species_eggshell_conductance_data.csv) to run R markdown scripts for phylogenetic comparative analysis and create phylogenetic tree diagrams and figures.<br><b>Species eggshell conductance phylogeny files:</b>The nexus (nex) tree file (tree_birdtree.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>The newick (nwk) tree file (species_eggshell_conductance_phylogeny.nwk) is the maximum clade credibility tree generated from the "R Markdown Phylogenetic Comparative Analysis" script. This tree is used for phylogenetic comparative analysis and to create the phylogenetic tree diagrams in the paper.<br><b>R script for Phylogenetic Comparative analysis: </b>The "R Markdown_Phylogenetic Comparative Analysis.Rmd" file measures phylogenetic signal and runs PGLS models for eggshell conductance. It also creates figures that assess collinearity. <br><br><b>R script for Phylogenetic tree diagrams and figures: </b>The "R Markdown_Figures and Phylogenetic Tree Diagram.Rmd" file creates phylogenetic tree diagrams, hybrid boxplots and scatterplots included in this paper. <br><b><br></b><b>FOLDER 2: COTURIX JAPONICA CONDUCTANCE BLOW HOLE VALIDATION</b><b><br></b>Previous eggshell conductance studies used eggshell fragments from another species to seal the blow hole of intact eggshells once they were filled with water. To prevent DNA contamination of museum eggshells used in our study, we considered plastic and parafilm as alternatives to seal the blow hole. We collected data on Japanese quail (<i>Coturix japonica</i>) eggs using different blow hole seals to test the reliability of eggshell conductance measurements. The data and R script used to assess repeatability of water loss over time using each blow hole treatment. Results of this validation experiment are provided in section (c) of Supplementary Information. <b><br></b><b>FOLDER 3: SPATIAL DISTRIBUTION TRAITS FOLDER</b><br>This folder contains the R markdown script ("R markdown_Species Distribution GH20 map.Rmd") and all shapefiles required to map global variation in water vapour conductance (<i>G</i>_H2O­) among avian eggs (Figure S2 of Supplementary Information). <br><b><br></b><br>