DOI: 10.5061/dryad.2ngf1vj0x
title: Data from: A wide range of abiotic and biotic variables leaves most variation in bird nest architecture unexplained

description: Nests are the locations or containers for offspring, and mediate
 interactions between offspring and the environment. However, understanding
 how environmental factors shape the evolution of nest architecture is
 complicated. In particular, the relative contributions of biotic (e.g.,
 protection from predation) and abiotic (e.g., microclimate maintenance)
 factors to the evolution of nest architecture have not been clearly
 quantified, and multiple nest traits, such as their location or shape, are
 rarely considered together. Here, we use a dataset of 3,685 bird species
 with complete data across five different nest traits (out of a wider
 dataset of 10,528 species included in the repository), to characterise a
 multivariate ‘morphospace’ of nest architecture. We achieve this using
 ordination methods, namely a principal coordinate analysis. Then, we use
 all derived axes of variation in nest morphospace and multivariate
 phylogenetic comparative methods used for geometric data to explore
 whether abiotic or biotic factors better explain the variation observed in
 ordination-derived nest architecture. We detect that abiotic
 environmental factors (climate) explain more variation than biotic
 factors. However, substantial variation in nest architecture remains
 unexplained after accounting for the variables used here, suggesting that
 commonly used nest traits may not capture covariation between nest
 architecture and the environment as expected. Nonetheless, our study
 demonstrates how nest evolution is affected by the environment on a global
 scale, which will form a foundation to explore a more diverse array of
 nest traits and environmental variables, to understand nest evolution in
 the world’s birds.
description: # Title of Dataset 'A wide range of abiotic and biotic variables
 leave most variation in bird nest architecture unexplained' Access
 this dataset at DRYAD: The dataset contains all information, including
 original data, directions to third-party datasets, and R scripts necessary
 to replicate all of the datasets, results and figures reported in the
 manuscript 'A wide range of abiotic and biotic variables leave most
 variation in bird nest architecture unexplained' submitted to Proc
 Roy Soc B. ## Description of the data and file structure Code in the
 different subrepositories should be run in order of the numbers of
 subrepositories (01-06). All original datafile have their column
 descriptions. Third party data is provided with links to download pages
 with associated metadata (not provided here unless altered). NB: this
 repository is provided clean of outputs. All scripts need to be run in
 order to generate outputs. All files below need to be included, and
 correctly named, for the entire repository to execute correctly. Running
 script 01_DATA.R is not necessary as its output is provided, as 01_DATA.R
 is time and memory intensive, whilst other scripts are not. Directory
 structure: nest/ (parent directory) \- BirdNest_TableS1; a TXT file table
 containing family level overview of the no. of species present in full
 nest dataset and the morphospace dataset (n = 3,685 species). Output of
 03_MORPH/03_MORPH.R provided here as a supplementary file. Cols: order
 (taxonomic order according to Clements taxonomy) family (taxonomic order
 according to Clements taxonomy) n (no. of species in the nest dataset
 collected (nest/01_DATA/data/nests_dataset.csv)) n_pcoa (no. of species in
 the morphospace dataset used for analyses
 (nest/analysis-read_nest_env_data.csv); also output of
 nest/01_DATA/01_DATA.R) \- 01_DATA/
 \============================================================================================ \- 01_DATA.R; original script necessary for data processing; NB: this is memory and time heavy script. Ideally run in a cluster environment for 24h with ~150G of RAM. However, it is possible to run it on a normal desktop if loops inside the script are broken/parallelised (not provided in the script). The output of this script - the CSV file analysis-read_nest_env_data.csv is provided, so this script does not need to be run to quickly recreate results. \======================================================================================== \- bin/ ``` - PRED_birds.gpkg; GPKG vector file created by 01_DATA.R, containing distributions of potential avian predators. Cols: birdlife (binomial name in IUCN [International Union for Conservation of Nature] taxonomy); geom (geometry) - PRED_mammals.gpkg; GPKG vector file created by 01_DATA.R, containing distributions of potential mammalian predators. Cols: sci_name (binomial name in IUCN taxonomy); geom (geometry) - PRED_reptiles.gpkg; GPKG vector file created by 01_DATA.R, containing distributions of potential reptile predators. Cols: sci_name (binomial name in IUCN taxonomy); geom (geometry) - predatory_birds.csv; CSV file created by 01_DATA.R, containing names of potential avian predators. Cols: binomial (binomial name in IUCN taxonomy) - predatory_mammals.csv; CSV file created by 01_DATA.R, containing names of potential mammalian predators. Cols: binomial (binomial name in IUCN taxonomy) - predatory_reptiles.csv; CSV file created by 01_DATA.R, containing names of potential reptile predators. Cols: Species (binomial name in IUCN taxonomy) ======================================================================================== - biogeography_data/ - MODIS_NDVI_2001; repository containing monthly NDVI TIF files for year 2001 (closest to WorldClim); not provided due to being third party, download here: https://neo.gsfc.nasa.gov/view.php?datasetId=MOD_NDVI_M. - MOD_NDVI_M_2001_01_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_02_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_03_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_04_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_05_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_06_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_07_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_08_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_09_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_10_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_11_01_rgb_3600x1800.tif - MOD_NDVI_M_2001_12_01_rgb_3600x1800.tif - ne_10m_land/; repository for NaturalEarthData containing a shapefile of all land at 1:10,000,000 resolution; not provided due to being third party, file names unchanged from original at point of download, download at https://www.naturalearthdata.com/downloads/10m-physical-vectors/10m-land/. - ne_10m_land.cpg - ne_10m_land.dbf - ne_10m_land.prj - ne_10m_land.README - ne_10m_land.shp - ne_10m_land.shx - ne_10m_land.VERSION - wc2.1_10m_prec; repository containing WorldClim v2.1 precipitation data at 10 arcminutes resolution; original file naming retained at point of download; not provided due to being third part; download at: https://www.worldclim.org/data/worldclim21.html - wc2.1_10m_prec_01.tif - wc2.1_10m_prec_02.tif - wc2.1_10m_prec_03.tif - wc2.1_10m_prec_04.tif - wc2.1_10m_prec_05.tif - wc2.1_10m_prec_06.tif - wc2.1_10m_prec_07.tif - wc2.1_10m_prec_08.tif - wc2.1_10m_prec_09.tif - wc2.1_10m_prec_10.tif - wc2.1_10m_prec_11.tif - wc2.1_10m_prec_12.tif - wc2.1_10m_srad; repository containing WorldClim v2.1 insolation data at 10 arcminutes resolution; original file naming retained at point of download; not provided due to being third part; download at: https://www.worldclim.org/data/worldclim21.html - wc2.1_10m_srad_01.tif - wc2.1_10m_srad_02.tif - wc2.1_10m_srad_03.tif - wc2.1_10m_srad_04.tif - wc2.1_10m_srad_05.tif - wc2.1_10m_srad_06.tif - wc2.1_10m_srad_07.tif - wc2.1_10m_srad_08.tif - wc2.1_10m_srad_09.tif - wc2.1_10m_srad_10.tif - wc2.1_10m_srad_11.tif - wc2.1_10m_srad_12.tif - wc2.1_10m_tavg; repository containing WorldClim v2.1 temperature data at 10 arcminutes resolution; original file naming retained at point of download; not provided due to being third part; download at: https://www.worldclim.org/data/worldclim21.html - wc2.1_10m_tavg_01.tif - wc2.1_10m_tavg_02.tif - wc2.1_10m_tavg_03.tif - wc2.1_10m_tavg_04.tif - wc2.1_10m_tavg_05.tif - wc2.1_10m_tavg_06.tif - wc2.1_10m_tavg_07.tif - wc2.1_10m_tavg_08.tif - wc2.1_10m_tavg_09.tif - wc2.1_10m_tavg_10.tif - wc2.1_10m_tavg_11.tif - wc2.1_10m_tavg_12.tif - wc2.1_10m_vapr; repository containing WorldClim v2.1 water vapour pressure data at 10 arcminutes resolution; original file naming retained at point of download; not provided due to being third part; download at: https://www.worldclim.org/data/worldclim21.html - wc2.1_10m_vapr_01.tif - wc2.1_10m_vapr_02.tif - wc2.1_10m_vapr_03.tif - wc2.1_10m_vapr_04.tif - wc2.1_10m_vapr_05.tif - wc2.1_10m_vapr_06.tif - wc2.1_10m_vapr_07.tif - wc2.1_10m_vapr_08.tif - wc2.1_10m_vapr_09.tif - wc2.1_10m_vapr_10.tif - wc2.1_10m_vapr_11.tif - wc2.1_10m_vapr_12.tif - wc2.1_10m_wind; repository containing WorldClim v2.1 wind speed data at 10 arcminutes resolution; original file naming retained at point of download; not provided due to being third part; download at: https://www.worldclim.org/data/worldclim21.html - wc2.1_10m_wind_01.tif - wc2.1_10m_wind_02.tif - wc2.1_10m_wind_03.tif - wc2.1_10m_wind_04.tif - wc2.1_10m_wind_05.tif - wc2.1_10m_wind_06.tif - wc2.1_10m_wind_07.tif - wc2.1_10m_wind_08.tif - wc2.1_10m_wind_09.tif - wc2.1_10m_wind_10.tif - wc2.1_10m_wind_11.tif - wc2.1_10m_wind_12.tif ======================================================================================== - data/ - bird_elton.txt; EltonTraits dataset for bird species; not provided due to being third party; download at https://esajournals.onlinelibrary.wiley.com/doi/10.1890/13-1917.1 - elton_names_birds.csv; CSV file containing a crosswalk between taxonomy of EltonTraits and IUCN for birds. Cols: Scientific (binomial name as in bird_elton.txt); binomial (binomial name based on IUCN taxonomy, as used in IUCN shapefiles). - elton_names_mammals.csv; CSV file containing a crosswalk between taxonomy of EltonTraits and IUCN for mammals. Cols: Scientific (binomial name as in bird_elton.txt); binomial (binomial name based on IUCN taxonomy, as used in IUCN shapefiles). - mammal_elton.txt; EltonTraits dataset for mammal species; not provided due to being third party; download at https://esajournals.onlinelibrary.wiley.com/doi/10.1890/13-1917.1 - nests_dataset.csv; CSV file containing all original nest data collected for this manuscript. See Methods for additional explanations. Missing values are present in this dataset and indicated with row value 'NA'. Data is missing due to either not being available in the BOW account at the time of data collection, or being unclear/dubious (see Methods in the manuscript). The scripts in this repository will explicitly handle 'NA' as missing values and no modification is needed. Cols: order (taxonomic order according to Clements taxonomy); family (taxonomic family according to Clements taxonomy); clements (binomial species name according to Clements taxonomy); jetz (binomial species name according to birdtree.org); birdlife (binomial species name according to IUCN/Birdlife taxonomy); is (binomial term coded Y/N, indicating island endemicity; Y - island endemic; N - breeding on continents) loc (main continent inhabited by the bird species) realm (biogeographic realm inhabited by the bird species) iucn (IUCN status; codes used: LC/NT/VU/EN/CR/EW/EX) type (nest type, see Methods) str (nest structure, see Methods) site (nest site, see Methods) att (nest attachment, see Methods) hmin (minimum nest height (meters), see Methods) bodmax (maxmimum body mass (grams), see Methods) hmax (maximum nest height (meters), see Methods) bodmin (minimum body mass (grams), see Methods) dich (binomial term coded y/n, indicating sexual dichromatism in the species; Y - sexually dichromatic; N - not sexually dichromatic, see Methods) - ReptTraits dataset v1-2.csv; CSV file containing a dataset of diet of reptiles; not provided due to being third party; download at https://www.nature.com/articles/s41597-024-03079-5 - seabirds.csv; CSV file containing names of birds classified as seabirds (see Methods). Cols: order (taxonomic order according to Clements taxonomy); family (taxonomic family according to Clements taxonomy); name (common name as shown in Birds of the World); genus (latin generic name according to Clements taxonomy); species (latin specific name according to Clements taxonomy); sea (categorical variable with three states, indicating the habitat of the seabird; states are: coastal | offshore | pelagic) ======================================================================================== - iucn_shapefiles/ Directory contains shapefiles of ranges of reptiles and mammals, as downloaded from IUCN; not provided due to being third party; download at: https://www.iucnredlist.org/resources/spatial-data-download - CROCODILES_ALLIGATORS/ - CROCODILES_ALLIGATORS.cpg - CROCODILES_ALLIGATORS.dbf - CROCODILES_ALLIGATORS.id_no.atx - CROCODILES_ALLIGATORS.prj - CROCODILES_ALLIGATORS.sbn - CROCODILES_ALLIGATORS.sbx - CROCODILES_ALLIGATORS.shp - CROCODILES_ALLIGATORS.shx - MAMMALS_FRESHWATER/ - MAMMALS_FRESHWATER.cpg - MAMMALS_FRESHWATER.dbf - MAMMALS_FRESHWATER.id_no.atx - MAMMALS_FRESHWATER.prj - MAMMALS_FRESHWATER.sbn - MAMMALS_FRESHWATER.sbx - MAMMALS_FRESHWATER.shp - MAMMALS_FRESHWATER.shx - MAMMALS_MARINE_AND_TERRESTRIAL/ - MAMMALS_MARINE_AND_TERRESTRIAL.cpg - MAMMALS_MARINE_AND_TERRESTRIAL.dbf - MAMMALS_MARINE_AND_TERRESTRIAL.id_no.atx - MAMMALS_MARINE_AND_TERRESTRIAL.prj - MAMMALS_MARINE_AND_TERRESTRIAL.sbn - MAMMALS_MARINE_AND_TERRESTRIAL.sbx - MAMMALS_MARINE_AND_TERRESTRIAL.shp - MAMMALS_MARINE_AND_TERRESTRIAL.shx - MAMMALS_TERRESTRIAL_ONLY/ - MAMMALS_TERRESTRIAL_ONLY.cpg - MAMMALS_TERRESTRIAL_ONLY.dbf - MAMMALS_TERRESTRIAL_ONLY.id_no.atx - MAMMALS_TERRESTRIAL_ONLY.prj - MAMMALS_TERRESTRIAL_ONLY.sbn - MAMMALS_TERRESTRIAL_ONLY.sbx - MAMMALS_TERRESTRIAL_ONLY.shp - MAMMALS_TERRESTRIAL_ONLY.shx - SCALED_REPTILES/ - SCALED_REPTILES_PART1.cpg - SCALED_REPTILES_PART1.dbf - SCALED_REPTILES_PART1.id_no.atx - SCALED_REPTILES_PART1.prj - SCALED_REPTILES_PART1.sbn - SCALED_REPTILES_PART1.sbx - SCALED_REPTILES_PART1.shp - SCALED_REPTILES_PART1.shx - SCALED_REPTILES_PART2.cpg - SCALED_REPTILES_PART2.dbf - SCALED_REPTILES_PART2.id_no.atx - SCALED_REPTILES_PART2.prj - SCALED_REPTILES_PART2.sbn - SCALED_REPTILES_PART2.sbx - SCALED_REPTILES_PART2.shp - SCALED_REPTILES_PART2.shx - TUATARA/ - data_0.cpg - data_0.dbf - data_0.prj - data_0.shp - data_0.shx - TURTLES/ - TURTLES.cpg - TURTLES.dbf - TURTLES.id_no.atx - TURTLES.prj - TURTLES.sbn - TURTLES.sbx - TURTLES.shp - TURTLES.shx ======================================================================================== ============================================================================================ - 02_PHYLO/ - 02_PHYLO.R; original R script matching species names in the dataset output of 01_DATA.R (analysis-read_nest_env_data.csv; also provided seperately). This script takes ~ 1 minute to run. ======================================================================================== - data/ - Clements2021_MCC.tre; a tree file with a maximum clade credibility tree of all bird species in Clements 2021 taxonomy. Not provided due to being third party; download at: https://www.pnas.org/doi/10.1073/pnas.2409658122 ======================================================================================== ======================================================================================== - 03_MORPH/ - 03_MORPH.R; original R script performing the principal coordinate analysis on nest architecture data; generating principal components of climate; plotting sub-figures of Figure 1, Figure S1, S2 and S4; outputting results presented in Results, Table S4. Takes ~10 minutes to run. ======================================================================================== - bin/ (empty, to store outputs from 03_MORPH.R) ======================================================================================== - figs/ (empty subdirectories, to store outputs from 03_MORPH.R - Figure 1/ (will store subplots of Figure 1) - Figure S1/ (will store subplots of Figure S1) - Figure S2/ (will store subplots of Figure S4) - Figure S3/ (will store subplots of Figure S2) ======================================================================================== ======================================================================================== - 04_PRED/ - 04_PRED.R; original R script to test the correlation between predator diversity data (obtained in 01_DATA.R) and data on daily nest predation. Script takes ~1 minute to run. ======================================================================================== - data/ - PNAS_nest_predation_data.csv; a CSV file containing a dataset on daily nest predation for multiple bird species; not provided due to being third party. Download at: https://www.pnas.org/doi/10.1073/pnas.2402652121. ======================================================================================== - figs/ (empty subdirectory to hold Figure S3) ======================================================================================== ======================================================================================== - 05_ENV/ - 05_ENV.R; original R script containing the code for the analysis of correlations of nest morphospace with the environment. Script takes about ~30 minutes to run. ======================================================================================== - bin/ (empty to hold outputs of 05_ENV.R) ======================================================================================== - figs/ (empty subdirectories to hold outputs of 05_ENV.R) - Figure 1/ (empty to hold subfigures of Figure 2); NB: numbering is for figures generated by the script, with order of figures in the manuscript being different. - Figure 2/ (empty to hold subfigures of Figure 3) - 06_LOGI/ - 06_LOGI.R; original R script containing the code for univariate analyses of the nest dataset. Script takes about ~15 minutes to run. ``` ## Sharing/Access information All links have been provided in the descriptions of repositories. Additional list of links: IUCN range data - [https://www.iucnredlist.org/resources/spatial-data-download](https://www.iucnredlist.org/resources/spatial-data-download) NaturalEarth data - [https://www.naturalearthdata.com/downloads/10m-physical-vectors/10m-land/](https://www.naturalearthdata.com/downloads/10m-physical-vectors/10m-land/) WorldClim data - [https://www.worldclim.org/data/worldclim21.html](https://www.worldclim.org/data/worldclim21.html) MODIS data - [https://neo.gsfc.nasa.gov/view.php?datasetId=MOD_NDVI_M](https://neo.gsfc.nasa.gov/view.php?datasetId=MOD_NDVI_M). Nest predation data - [https://www.pnas.org/doi/10.1073/pnas.2402652121](https://www.pnas.org/doi/10.1073/pnas.2402652121). ReptTraits data - [https://www.nature.com/articles/s41597-024-03079-5](https://www.nature.com/articles/s41597-024-03079-5) EltonTraits data - [https://esajournals.onlinelibrary.wiley.com/doi/10.1890/13-1917.1](https://esajournals.onlinelibrary.wiley.com/doi/10.1890/13-1917.1) ## Code/Software R (and optionally RStudio) are needed to run all analyses. Every original RScript is described in the repository structure. The repositories and RScript follow a numerical order of 1-6, signposted as 01\_ - 06\_ prefix to each repository. On first run, they need to be run in that order to generate dependent files. ## Version changes 06-10-2025. Scripts 03_MORPH.R and 05_ENV.R updated to include cosmetic changes to plots (use of en-dash; use of scientific notation) requested by the journal typesetter. Additionally, code in previous 05_ENV.R was accidentally uploaded outdated, and did not scale explanatory variables, as present in the accepted manuscript. The necessary line of code has been added.