Rolland V.*, Grindstaff J., Balenger S., and Siefferman L.

*Corresponding author: vrolland@astate.edu 

https://doi.org/10.5061/dryad.2ngf1vhwh

Descripiton of the data files

This document describes columns in Excel files used for the study of natural selection in Eastern Bluebirds that survived the 2021 snowstorms in the south-central US. Only fatalities encountered in nest boxes were included in the first file, but both fatalities and survivors caught during the nesting season that followed the storms are included in the second file. Scripts are for analyses in Program R. Scripts for analyses were run in Program R version 4.4.1 on Windows 11 x64.

Responsibilities

·         Data collection: Rolland (AR), Grindstaff (OK), Balenger (MS) collected feathers from and measured dead and live bluebirds

·         Feather data: Siefferman (NC) prepared and analyzed feathers for coloration variables

·         R Code: Rolland compiled the data and wrote the code

Data structure

Repeatability_MasterData_for_AmNat.csv

This file includes measurements on various bluebird morphological traits. When a bird was missing a tail feather, we entered an NA value, which was also necessary for the asymmetry variable. Similarly, if a bird was in poor condition (e.g., bent wing, degraded bill), we used NA as a value for the impacted variable. We used the file to determine whether our measurements were accurate through an analysis of repeatability of three sets of measurements on the same traits. Columns are as defined as follows:

·         State: two-letter code for US state

·         Bird: Unique bird ID number. If a bird was already banded, its ID was the band number. If not previously banded, the number was made up with a site-specific system.

·         Sex: Two-category variable with F for female and M for male

·         Round: Each bird was measured three times in a random order each time. Round refers to the first, second, or third round of measurements.

·         Wleft and Wright: Relaxed wing chord for left and right wings measured in mm.

·         Wasym: Absolute difference in wing chord (mm) between left and right wings.

·         Bwidth, Blength, and Bdepth: Beak width, length, and depth measured in mm.

·         Lleft and Lright: Tarsus length for left and right tarsus in mm.

·         Lasym:  Absolute difference in tarsus length (mm) between left and right legs (tarsi).

·         Tleft and Tright: Left and right outermost tail feather (rectrix R6) length in mm.

·         Tmiddle: Middle tail feather length (rectrix R1) in mm

·         Tasym: Absolute difference in length (mm) of outermost tail feathers (rectrices R6) between left and right.

Natural Selection_MasterData_for_AmNat.csv

This file includes raw and derived measurement for various bluebird morphological and plumage coloration traits. When a bird was missing a tail feather, we entered an NA value, which was also necessary for the asymmetry variable. Similarly, if a bird was in poor condition (e.g., bent wing, degraded bill, bare belly), we used NA as a value for the impacted variable. We used the file to determine if natural selection occurred and on which traits through various approaches (model selection, principal component analysis, and selection gradients/differentials). Columns are as defined as follows:

Demographic data

·         State: two-letter code for US state

·         Box: Nest box ID in which a fatality was collected or at which a survivor was captured during a nesting attempt.

·         Sex: Two-category variable with F for female and M for male

·         BirdID: Unique bird ID number. If a bird was already banded, its ID was the band number. If not previously banded, the number was made up with a site-specific system.

·         Survived: Binary variable to indicate whether a bird was measured as a fatality (N) or as a live bird (Y).

·         Recap?: Binary variable to indicate whether a bird had been previously banded and therefore  measured as a recaptured bird (Y) or as a new individual (N).

Morphological traits

·         WCleft and WCright: Relaxed wing chord for left and right wings measured in mm.

·         BW, BL, and BD: Beak width, length, and depth measured in mm.

·         TRleft and TRright: Tarsus length for left and right tarsus in mm.

·         TLleft and TLright: Left and right outermost tail feather (rectrix R6) length in mm.

·         TLmiddle: Middle tail feather length (rectrix R1) in mm

·         BV ** and **BS: Beak volume (mm3) and beak surface area (mm2) calculated from values of beak depth, width, and length, using volume and surface area formulas for an elliptic cone.

Plumage coloration traits

·         BellyB: Belly brightness (total amount of light reflected by the feather) measured as the summed reflectance (over 5 readings of 20 reflectance curve per reading) in nm from 6–8 feathers of the white belly region from each bird.

·         BreastB: Breast brightness (total amount of light reflected by the feather) measured as the summed reflectance (over 5 readings of 20 reflectance curve per reading) in nm from 6–8 feathers of the chestnut breast region from each bird.

·         BreastRC: Breast red chroma measured as the ratio of the total reflectance in the red range to the total reflectance of the entire spectrum (∫645-700/∫300-700) using 6–8 feathers from the chestnut breast region of each bird.

·         RumpB: Rump brightness (total amount of light reflected by the feather) measured as the summed reflectance (over 5 readings of 20 reflectance curve per reading) in nm from 6–8 feathers of the blue rump region from each bird.

·         RumpUVC: Rump UV chroma (spectral purity) measured as the ratio of the total reflectance in the ultraviolet range to the total reflectance of the entire spectrum (∫300-400/∫300-700) using 6–8 feathers from the blue rump region of each bird.

·         RumpH: Rump hue measured as the wavelength (nm) at peak reflectance, from 6–8 feathers from the blue rump region of each bird.

·         TailB: Belly brightness (total amount of light reflected by the feather) measured as the summed reflectance (over 5 readings of 20 reflectance curve per reading) in nm from the right outer tail feather (rectrix R6) from each bird.

·         TailUVC: Tail UV chroma (spectral purity) measured as the ratio of the total reflectance in the ultraviolet range to the total reflectance of the entire spectrum (∫300-400/∫300-700) using the right outer rectrix of each bird.

·         TailH: Tail hue measured as the wavelength (nm) at peak reflectance, from the outer rectrix of each bird.

Code

Repeatability analyses_script_for_AmNat.r

This file contains the code used to run the repeatability analyses based on data in Repeatability_MasterData_for_AmNat.csv described above. The only package used is rptR version 0.9.22.

Natural selection analyses_script_for_AmNat.r

This file uses the file labeled Natural selection_MasterDara_for_AmNat.csv described above. The code assumes that this script is saved in the same folder as the csv file. If not, the user will need to properly set the working directory.

After a list of packages and some code to import and prepare the data, this file of codes is organized by analysis in the same order as analyses appear in the manuscript. Headings are collapsible for a sort of Table of Content, which can also be found in the drop-down menu in the bottom edge of the script window in RStudio for an easier navigation among sections. The code for the figures presented in the manuscript is embedded in this script under their respective analyses as well as references to Tables and manuscript sections/paragraphs.

Packages used in this script are as listed alphabetically with their version below:

·         ade4                version 1.7-22

·         AICcmodavg  version 2.3-3

·         corrplot            version 0.92

·         effects             version 4.2-2

·         emmeans         version 1.10.3

·         factoextra        version 1.0.7

·         FactoMineR    version 2.11

·         ggeffects         version 1.7.0

·         ggplot2            version 3.5.1

·         ggpubr             version 0.6.0

·         lme4                version 1.1-35.5