DOI: 10.5061/dryad.2547d7wzq
title: Seasonality structures avian functional diversity and niche packing across North America

description: Assemblages in seasonal ecosystems undergo striking changes in species
 composition and diversity across the annual cycle. Despite a long-standing
 recognition that seasonality structures biogeographic gradients in
 taxonomic diversity (e.g., species richness), our understanding of how
 seasonality structures other aspects of biodiversity (e.g., functional
 diversity) has lagged. Integrating seasonal species distributions with
 comprehensive data on key morphological traits for bird assemblages across
 North America, we find that seasonal turnover in functional diversity
 increases with the magnitude and predictability of seasonality.
 Furthermore, seasonal increases in bird species richness led to a denser
 packing of functional trait space, but functional expansion was important,
 especially in regions with higher seasonality. Our results suggest that
 the magnitude and predictability of seasonality and total productivity can
 explain the geography of changes in functional diversity with broader
 implications for understanding species redistribution, community assembly,
 and ecosystem functioning. 
description: # Seasonality structures avian functional diversity and niche packing
 across North America
 [https://doi.org/10.5061/dryad.2547d7wzq](https://doi.org/10.5061/dryad.2547d7wzq) The following repository includes processed data and code necessary to repeat analyses for the manuscript: Keyser, S. R., Pauli, J. N., Fink, D., Radeloff, V. C., Pigot, A. L., and B. Zuckerberg. Seasonality Structures Avian Functional Diversity and Niche Packing Across North America. ## Description of the data and file structure The following data and code is shared as a R Project. The data files list below are contained within the "Data" subfolder of the RProject. Seasonal_FD_Dat_Final.csv contains information on the 5000 randomly sampled sites that were analyzed in the manuscript. Columns: Site: Unique identifier for each point location lat: Point latitude in WGS84 (EPSG: 4326) for each location. Unit: Decimal degree long: Point longitude in WGS84 (EPSG: 4326) for each location. Unit: Decimal degree BCR: Intersecting Bird Conservation Region for each location. Numerical code for corresponding Bird Conservation Region. sr.bs: Species richness of the breeding season (Northern Hemisphere summer) for each location. Expressed as number of species at a site during the breeding season. sr.nb: Species richness of the nonbreeding season (Northern Hemisphere winter) for each location. Expressed as number of species at a site during the nonbreeding season. volume.bs: Breeding season functional richness for each location. Expressed as volume of the breeding season trait space (SD^3). volume.nb: Nonbreeding season functional richness for each location. Expressed as volume of the nonbreeding season tratis space (SD^3). SES.volume.bs: Standardized effect size for breeding season functional richness for each location. Unitless value showing functional richness deviation from 100 null communities. SES.volume.nb: Standardized effect size for nonbreeding season functional richness for each location. Unitless value showing functional richness deviation from 100 null communities. f.btot: Total seasonal functional beta diversity estimate for each location. Values range from 0 (indentical functional volumes) to 1 (completely disjunct functional volumes). f.brich: Richness component of seasonal functional beta diversity estimate for each location. Values range from 0 (indentical functional volumes) to 1 (completely disjunct functional volumes). f.brep: Replacement component of seasonal functional beta diversity estimate for each location. Values range from 0 (indentical functional volumes) to 1 (completely disjunct functional volumes). fmpd.bs: Mean pair-wise distance for species in three-dimensional PCA space during the breeding season for each location. Average distance in PCA space between all possible pairwise combinations. fmpd.nb: Mean pair-wise distance for species in three-dimensional PCA space during the nonbreeding seas for each location. Average distance in PCA space between all possible pairwise combinations. SES.f.tot: Standardized effect size for total seasonal functional beta diversity estimate for each location. Unitless value representing total functional beta diversity deviation from functional beta diversity estimated from 100 null communities. SES.f.brich: Standardized effect size for richness component of seasonal functional beta diversity estimate for each location. Unitless value representing richness component of functional beta diversity deviation from functional beta diversity (richness component) estimated from 100 null communities. SES.f.brep: Standardized effect size for replacement component of seasonal functional beta diversity estimate for each location. Unitless value representing replacement component functional beta diversity deviation from functional beta diversity (replacement component) estimated from 100 null communities. PropUniquePacking.hv: Proportion of unique seasonal niche packing for each location. Unit: Proportion of unique species contributing to packing (ranges from 0 to 1). PropTotalPacking.hv: Proportion of total seasonal niche packing for each location. Unit: Proportion of total species contributing to packing (ranges from 0 to 1). sea.scale: Scaled annual coefficient of variation of productivity. tp.scale: Scaled annual cumulative productivity. PrP.scale: Scaled inter-annual predictability of productivity. TR.scale: Scaled temperature range. PrT.scale: Scaled inter-annual predictability of temperature. Seasonal_FD_Dat_PassOnly_Final.csv contains information on the 5000 randomly sampled sites that were analyzed in the manuscript. This dataset corresponds only to species classified in order Passeriformes. Site: Unique identifier for each point location lat: Point latitude in WGS84 (EPSG: 4326) for each location. Unit: Decimal degree long: Point longitude in WGS84 (EPSG: 4326) for each location. Unit: Decimal degree BCR: Intersecting Bird Conservation Region for each location. Numerical code for corresponding Bird Conservation Region. sr.bs: Species richness of the breeding season (Northern Hemisphere summer) for each location. Expressed as number of species at a site during the breeding season. sr.nb: Species richness of the nonbreeding season (Northern Hemisphere winter) for each location. Expressed as number of species at a site during the nonbreeding season. volume.bs: Breeding season functional richness for each location. Expressed as volume of the breeding season trait space (SD^3). volume.nb: Nonbreeding season functional richness for each location. Expressed as volume of the nonbreeding season tratis space (SD^3). SES.volume.bs: Standardized effect size for breeding season functional richness for each location. Unitless value showing functional richness deviation from 100 null communities. SES.volume.nb: Standardized effect size for nonbreeding season functional richness for each location. Unitless value showing functional richness deviation from 100 null communities. f.btot: Total seasonal functional beta diversity estimate for each location. Values range from 0 (indentical functional volumes) to 1 (completely disjunct functional volumes). f.brich: Richness component of seasonal functional beta diversity estimate for each location. Values range from 0 (indentical functional volumes) to 1 (completely disjunct functional volumes). f.brep: Replacement component of seasonal functional beta diversity estimate for each location. Values range from 0 (indentical functional volumes) to 1 (completely disjunct functional volumes). fmpd.bs: Mean pair-wise distance for species in three-dimensional PCA space during the breeding season for each location. Average distance in PCA space between all possible pairwise combinations. fmpd.nb: Mean pair-wise distance for species in three-dimensional PCA space during the nonbreeding seas for each location. Average distance in PCA space between all possible pairwise combinations. SES.f.tot: Standardized effect size for total seasonal functional beta diversity estimate for each location. Unitless value representing total functional beta diversity deviation from functional beta diversity estimated from 100 null communities. SES.f.brich: Standardized effect size for richness component of seasonal functional beta diversity estimate for each location. Unitless value representing richness component of functional beta diversity deviation from functional beta diversity (richness component) estimated from 100 null communities. SES.f.brep: Standardized effect size for replacement component of seasonal functional beta diversity estimate for each location. Unitless value representing replacement component functional beta diversity deviation from functional beta diversity (replacement component) estimated from 100 null communities. PropUniquePacking.hv: Proportion of unique seasonal niche packing for each location. Unit: Proportion of unique species contributing to packing (ranges from 0 to 1). PropTotalPacking.hv: Proportion of total seasonal niche packing for each location. Unit: Proportion of total species contributing to packing (ranges from 0 to 1). sea.scale: Scaled annual coefficient of variation of productivity. Expressed in unit variance around the mean. tp.scale: Scaled annual cumulative productivity. Expressed in unit variance around the mean. PrP.scale: Scaled inter-annual predictability of productivity. Expressed in unit variance around the mean. TR.scale: Scaled temperature range. Expressed in unit variance around the mean. PrT.scale: Scaled inter-annual predictability of temperature. Expressed in unit variance around the mean. TraitPCA_All.csv contains the list of species used in this analysis with the PCA scores used in analyses in the manuscript. Columns: species_eBird: Species binomial nomenclature used by eBird taking from the 2019 Clements taxonomy. english_name: Species english name eBird_species_code_2019: Unique species identifier used by eBird order: Taxonomic classification for species to the order level (e.g., Passeriformes) family: Taxonomic classification for species to the family level (e.g., Fringillidae) Columns 6:14: PC scores for species for all 9 axes. Note: Only PC1-3 are used in analyses for this manuscript. TraitPCA_Passerines.csv contains the list of passerine species used in this analysis with the PCA scores used in analyses in the manuscript. Columns: species_eBird: Species binomial nomenclature used by eBird taking from the 2019 Clements taxonomy. english_name: Species english name eBird_species_code_2019: Unique species identifier used by eBird order: Taxonomic classification for species to the order level (e.g., Passeriformes) family: Taxonomic classification for species to the family level (e.g., Fringillidae) Columns 6:14: PC scores for species for all 9 axes. Note: Only PC1-3 are used in analyses for this manuscript. RandomSample_5000_OccurrenceMean_SpSpecific.csv contain raw data on the extracted species-specific occurrence probabilities for summer and winter season. Columns: Site: Unique identifier for the point location lat: Point latitude in WGS84 (EPSG: 4326) long: Point longitude in WGS84 (EPSG: 4326) BCR: Bird Conservation Region for the individual point location Columns 5:1054: Species occurrence probabilities for winter (e.g., "abetow_winter") and summer (e.g., "abetow_summer"). eBird species codes are followed by "_" and the season. Mean occurrence probabilities (range 0 to 1) for the species summer and winter season at a corresponding site. RandomSample_5000_OccurrenceMean_PasserineOnly.csv contain raw data on the extracted passerine species-specific occurrence probabilities for summer and winter season. Columns: Site: Unique identifier for the point location lat: Point latitude in WGS84 (EPSG: 4326) long: Point longitude in WGS84 (EPSG: 4326) BCR: Bird Conservation Region for the individual point location Columns 5:1054: Species occurrence probabilities for winter (e.g., "abetow_winter") and summer (e.g., "abetow_summer"). eBird species codes are followed by "_" and the season. Mean occurrence probabilities (range 0 to 1) for the species summer and winter season at a corresponding site. SpeciesRelativeContributions.csv contains species-level contributions to assemblage functional diversity. Columns: Site: Unique identifier for the point location Season: Character value indicating species seasonal presence at the site. Values include: "summer", "winter", "both". Species: Scientific name (Genus, Species) for the species. Contribution: Species-specific contribution to the assemblage (site-level) total functional richness for the entire year. Note: Sum of all "Contribution" values for all species will equal total functional richness for the assemblage across all seasons. ContributionRel: Species-specific relative contribution to the assemblage (site-level) functional richness for the entire year. Note: Sum of all "ContributionRel" values for all species will sum to 1 for the assemblage across all seasons. Method: Method used to estimate functional space (i.e., "hypervolume").  NA_Boundary.shp is the shapefile and associated data necessary for reproducing spatial mesh for INLA models in "Seasonal_FD_INLA_Analysis.R" and Seasonal_FD_Inla_Analysis_PassOnly.R". NA_Plotting.shp is the shapefile and associated data necessary for plotting in "FD_Summaries_Plotting.R" and "FD_Summaries_Plotting_PasserineOnly.R". Note: Missing values in any of the above data files will be read into R as "NA" and ignored in subsequent analyses. NAs arise from missing environmental data and assemblages with too few species to estimate functional diversity metrics. For analyses run in "SeasonalFD_INLA_Analysis.R" 7 out of 5000 random sites were dropped (0.1% of sites). For analyses run in "SeasonalFD_INLA_Analysis_PassOnly.R" 10 out of 5000 random sites were dropped (0.2% of sites).      Code listed below belongs in the remaining subdirectories of the project. ## Sharing/Access information Data was derived from the following sources: * [eBird Status and Trends](https://science.ebird.org/en/status-and-trends) * [AVONET](https://figshare.com/s/b990722d72a26b5bfead) * [Dynamic Habitat Indices](https://silvis.forest.wisc.edu/data/dhis/) * [Daymet (accessed via Google Earth Engine)](https://developers.google.com/earth-engine/datasets/catalog/NASA_ORNL_DAYMET_V4) ## Code/Software All code and data is provided in the Seasonal_FD_EcolLttrs.zip compressed folder. Code provided was written and executed in R Version 4.4.1. Scripts included can be used to produce all of the results from Keyser et al. Seasonality structures avian functional diversity and niche packing across North America. Annotations are provided in the code. For further questions regarding code availability and analysis pertaining please see the corresponding author's GitHub page: [https://github.com/skeyser](https://github.com/skeyser). To ensure smooth operation users should first verify that their R version is concurrent with R Version 4.4.1. Prior to running code we advise running the script titled "SeasonalFD_PackagSetup.R" to restore the R package library for this analysis. After libraries are installed the scripts listed below can be executed. ### R Project Structure Seasonal_FD_EcolLttrs ┣ Analysis ┃ ┣ CWM_Code ┃ ┃ ┣ CWM_Trait_Clean.R ┃ ┃ ┗ CWM_Trait_CleanPasserine.R ┃ ┣ FD_Summaries ┃ ┃ ┣ FD_Summaries_Plotting.R ┃ ┃ ┗ FD_Summaries_Plotting_PasserineOnly.R ┃ ┣ INLA_Code ┃ ┃ ┣ SeasonalFD_INLA_Analysis.R ┃ ┃ ┗ SeasonalFD_INLA_Analysis_PassOnly.R ┃ ┗ Species_Contribution_PostProcess.R ┣ Data ┃ ┣ NA_Boundary.dbf ┃ ┣ NA_Boundary.prj ┃ ┣ NA_Boundary.shp ┃ ┣ NA_Boundary.shx ┃ ┣ NA_Plotting.cpg ┃ ┣ NA_Plotting.dbf ┃ ┣ NA_Plotting.prj ┃ ┣ NA_Plotting.sbn ┃ ┣ NA_Plotting.sbx ┃ ┣ NA_Plotting.shp ┃ ┣ NA_Plotting.shp.xml ┃ ┣ NA_Plotting.shx ┃ ┣ RandomSample_5000_OccurrenceMean_SpSpecific.csv ┃ ┣ RandomSample_5000_OccurrenceMean_SpSpecific_PasserineOnly.csv ┃ ┣ Seasonal_FD_Dat_Final.csv ┃ ┣ Seasonal_FD_Dat_PassOnly_Final.csv ┃ ┣ SpeciesRelativeContributions.csv ┃ ┣ TraitPCA_All.csv ┃ ┗ TraitPCA_Passerine.csv ┣ renv ┣ .Rhistory ┣ .Rprofile ┣ README.md ┣ renv.lock ┣ SeasonalFD_PackageSetup.R ┗ Seasonal_FD_EcolLttrs.Rproj SeasonalFD_PackageSetup.R Script is used to install packages used for this analysis. This script should be run first to ensure the code below runs smoothly. SeasonalFD_INLA_Analysis.R Script for running the spatial regression models described in the paper. Input data includes "Seasonal_FD_Dat_Clean.csv" and accompanying shapefile "NA_Boundary.shp" to delineate the boundary for creating the mesh. Marginal effects plots and effect size figures created in this script. SeasonalFD_INLA_Analysis_PassOnly.R Script for running the spatial regression models described in the paper for the passerine-only analyses. Input data includes "Seasonal_FD_Dat_PassOnly_Clean.csv" and accompanying shapefile "NA_Boundary.shp" to delineate the boundary for creating the mesh. Marginal effects plots and effect size figures created in this script. SpeciesContribution_PostProcess.R Script for examining average species contribution to seasonal functional richness across all sites and seasons. Script produces Fig. S15 in Supplemental Information.   CWM_Trait_Clean.R Script for calculating occurrence-weighted mean trait values for each community. Input data needed is "RandomSample_5000_OccurrenceMean_SpSpecific.csv", "Seasonal_FD_Dat_Final.csv", and "TraitPCA_All.csv". CWM_Trait_CleanPasserine.R Script for calculating occurrence-weighted mean trait values for each community for passerines-only. Input data needed is "RandomSample_5000_OccurrenceMean_PassOnly.csv", "Seasonal_FD_Dat_PassOnly_Final.csv", and "TraitPCA_Passerines.csv". FD_Metrics_Plotting.R Script for maps and plots of functional diversity metrics. Input data included "Seasonal_FD_Dat_Final.csv". FD_Metrics_Plotting_PasserineOnly.R Script for maps and plots of functional diversity metrics for passerine-only analysis. Input data included "Seasonal_FD_Dat_PassOnly_Final.csv". renv is a folder containing exact package versions to restore for running these scripts.