Data from: 3D habitat structure drives avian functional and trait diversity across North America
Data files
Apr 06, 2026 version files 443.85 MB
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2017_20000_supercomputer_distcorrected_spRich_combined_verB.csv
6.98 KB
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2017_distmodel_20000_FinalSuper_summary.csv
10.72 MB
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Chp1_FinalData_AllIndicies_UpdatedVoxel_4bins_repair_ShannonReplacementTry1_TotHorFrag_NEW_PCoA.csv
257.80 KB
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cmdscale.vector4.rds
836 B
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FDiv.png
244.25 KB
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FEven.png
237.66 KB
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FRich.png
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Key_spec_scinames.csv
10.35 KB
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MPD.png
242.34 KB
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MultiSp_DistModel_2017_20000run.rds
430.41 MB
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PC1.png
239.28 KB
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PC2.png
242.76 KB
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PC3.png
245.30 KB
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PC4.png
242.79 KB
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PD.png
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PlotNum_Key.csv
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README.md
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SpRich.png
237.33 KB
Abstract
Understanding how three-dimensional (3D) habitat structure drives biodiversity patterns is key to predicting how habitat alteration and loss will affect species and community-level patterns in the future. To date, few studies have contrasted the effects of 3D habitat composition with those of 3D habitat configuration on biodiversity, with existing investigations often limited to measures of taxonomic diversity (i.e., species richness). Here, we examined the influence of Light Detecting and Ranging (LiDAR)-derived 3D habitat structure–both its composition and configuration–on multiple facets of bird diversity. Specifically, we used data from the National Ecological Observatory Network (NEON) to test the associations between eleven measures of 3D habitat structure and avian species richness, functional and trait diversity, and phylogenetic diversity. We found that 3D habitat structure was the most consistent predictor of avian functional and trait diversity, with little to no effect on species richness or phylogenetic diversity. Functional diversity and individual trait characteristics were strongly associated with both 3D habitat composition and configuration, but the magnitude and the direction of the effects varied across the canopy, subcanopy, midstory, and understory vertical strata. Our findings suggest that 3D habitat structure influences avian diversity through its effects on traits. By examining the effects of multiple aspects of habitat structure on multiple facets of avian diversity, we provide a broader framework for future investigations on habitat structure.
https://doi.org/10.5061/dryad.t76hdr87q
Description of the data and file structure
This dataset contains the output data for this paper's main analysis. Included here are data from Bayesian distance sampling models, PCoA output data, species/plot keys, original figure outputs, and the final data file used to run the 120 Bayesian Mixed Effect Models.
Raw/original data were obtained from the following datasets:
- National Ecological Observatory Network (NEON) shapefiles: https://www.neonscience.org/data-samples/data/spatial-data-maps
- LiDAR Data: NEON data product: DP1.30003.001
- Breeding landbird point counts/Elevation/latitude: NEON data product DP1.10003.001
- Trait data: AVONET (Tobias et al. 2022) and EltonTraits 1.0 databases (Wilman et al. 2014).
- Temperature Range: Daymet (Thornton et al. 2022)
- Species range maps: BirdLife International (BirdLife International 2022)
- Phylogenetic Trees: Bird Tree (Jetz et al. 2012) - Ericson backbone
The dataset contains the following files:
1). MultiSp_DistModel_2017_20000run.rds: This file contains the original output of the multispecies distance model. This Bayesian model ran for 20,000 iterations and contained estimates of abundance that were modeled using the formulation outlined in the paper's supplemental materials. Mean estimates of individual species abundances were obtained from this file and used in subsequent analysis.
2). 2017_distmodel_20000_FinalSuper_summary.csv: This file contains the parameter estimates of each variable used in the multispecies distance model. Columns contain: variable (name of variable), mean (average parameter estimate), sd (standard deviation), credible intervals ranging from 2.5% to 97.5%, Rhat, n.eff (effective sample size), overlap0, and f.
3). 2017_20000_supercomputer_distcorrected_spRich_combined_verB.csv: A table summarizing the different species richness values before and after correcting abundances using distance sampling methods. Column contain: plotNum (unique avian plot number internal to this paper), Original_spRich (original species richness of 2017 data per plot), distcorr_1_SpRich (species richness calculated from the distance sampling model output using species containing mean abundance values greater than 1), distcorr_1_SpRich (species richness calculated from the distance sampling model output using species containing mean abundance values greater than 1 with species whose range falls outside of the NEON domain where an individual plot is located set to 0 to avoid improper model estimation), and distcorr_95_SpRich (species richness calculated from the distance sampling model output using species containing mean abundance values greater than 0.95 with species whose range falls outside of the NEON domain where an individual plot is located set to 0 to avoid improper model estimation).
4). cmdscale.vector4.rds: File containing the PCoA output.
5). Key_spec_scinames.csv: A table containing the 260 species used in this paper, identified by a unique species number (spec), scientific name, and common name. Note that different trait, phylogenetic, and range map datasets use different taxonomies, and thus, this key is used to standardize datasets throughout the analysis.
6). PlotNum_Key.csv: A table containing the 448 candidate plots used in this analysis (filtered down to 385 for the final analysis due to missing data or other methodological considerations). Columns contain: plotNum (unique avian plot number internal to this paper), domainID (NEON domain), siteID (NEON 4-letter site abbreviation), plotID (NEON unique plot ID identifier), decimalLatitude (latitude of plot centroid), decimalLongitude (longitude of plot centroid).
7). Figures: original/larger versions of final model output files, corresponding to Figure 4 in the main text. Each PNG file contains a different response variable and the parameter estimates (y-axis across all 12 models (key). Species Richness (SpRich.png), Faith's Phylogenetic Diversity (PD.png), Mean Pairwise Distance (MPD.png), Principle coordinate 1 (PC1.png), Principle coordinate 2 (PC2.png), Principle coordinate 3 (PC3.png), Principle coordinate 4 (PC4.png) , functional richness (FRich.png), functional evenness (FEven.png), Functional divergence (FDiv.png)
8). Chp1_FinalData_AllIndicies_UpdatedVoxel_4bins_repair_ShannonReplacementTry1_TotHorFrag_NEW_PCoA.csv: Final data file. Column names of final data file:
- plotID: NEON plotID
- plotNum: plot number (unique to this project only)
- domainID: NEON domain ID
- siteID: NEON site ID
- decimalLatitude: latitude of plot centroid
- decimalLongitude: longitude of plot centroid
- Original_SpRich: Uncorrected SpRichness 8: rangefilt_95_SpRich: species richness after distance sampling, filtered by species range, and only containing species with >95% prob of occurrence (as estimated by distance sampling model)
- FEve: functional evenness value
- FDiv: functional divergence value
- original_FRic: functional richness, not corrected for species richness
- SES.FRic: standard effect size of functional richness using 100 random communities (corrected for species richness)
- FRic.p: p-value of SES.FRic calculation
- original_PD: Faith's Phylogenetic Diversity, not corrected for species richness
- SES.PD: standard effect size of Faith's Phylogenetic Diversity using 100 random communities (corrected for species richness) 16: PD.p: p-value of SES.PD calculation
- original_MPD: Mean Pairwise Distance, not corrected for species richness
- SES.MPD: standard effect size of Mean Pairwise Distance using 100 random communities (corrected for species richness)
- MPD.p: p-value of MPD.p calculation
- nlcdClass: NLCD landcover classification of avian plot centroid (as reported by NEON)
- elevation: elevation of avian plot centroid (as reported by NEON)
- temp.range_CHELSA: temperature range (i.e., min-max) of the NEON avian survey period (May-June) during 2017 (NOT USED)
- temp.ave_CHELSA: average temperature of the NEON avian survey period (May-June) during 2017 (NOT USED)
- precip.annual_CHELSA: total annual precipitation during 2017 (NOT USED)
- temp.range_daymet: temperature range (i.e., min-max) of the NEON avian survey period (May-June) during 2017
- temp.ave_daymet: average temperature of the NEON avian survey period (May-June) during 2017 (NOT USED)
- precip.total_daymet: total annual precipitation during 2017 (NOT USED)
- Vert.Variance: OUT OF DATE METRIC (Kept for posterity)
- Vert.Shannon: OUT OF DATE METRIC (Kept for posterity)
- Vert.Simpson: OUT OF DATE METRIC (Kept for posterity)
- Vert.Mean: OUT OF DATE METRIC (Kept for posterity)
- volume_und: volume of understory (0-5m)
- volume_mid: volume of midstory (5-15m)
- volume_subcan: volume of subcan (15-25m)
- volume_can: volume of canopy (>25m)
- clumpy_und: clumpiness of understory horizontal raster (not used)
- clumpy_mid: clumpiness of midstory horizontal raster (not used)
- clumpy_subcan: clumpiness of subcanopy horizontal raster (not used)
- clumpy_can: clumpiness of canopy horizontal raster (not used)
- te_und: total edge of understory horizontal raster (not used)
- te_mid: total edge of understory horizontal raster (not used)
- te_subcan: total edge of subcanopy horizontal raster (not used)
- te_can: total edge of canopy horizontal raster (not used)
- np_und: number of patches of understory horizontal raster
- np_mid: number of patches of midstory horizontal raster
- np_subcan: number of patches of subcanopy horizontal raster
- np_can: number of patches of canopy horizontal raster
- Total_veg_amt_NEW: sum of all vegetation amount across all 4 vertical strata
- shannon_plot: vertical heterogeneity metric (not used)
- simpson_plot: vertical heterogeneity metric (not used)
- variance_plot: vertical heterogeneity metric (CURRENT)
- range_abs: custom vertical heterogeneity metric (not used)
- dist_traveled: custom vertical heterogeneity metric (not used)
- clumpy_TotVol: clumpiness of total volume raster (not used)
- np_TotVol: number of patches of total volume raster (2D configuration)
- te_TotVol: total edge of total volume raster (not used)
- PC1: principle component axes 1 value
- PC2: principle component axes 2 value
- PC3: principle component axes 3 value
- PC4: principle component axes 4 value
- VegRating: vegetation rating of each plot (understory, midstory, subcanopy, canopy), used for plotting
Sharing/Access information
Links to other publicly accessible locations of the data:
- National Ecological Observatory Network (NEON) shapefiles: https://www.neonscience.org/data-samples/data/spatial-data-maps
- LiDAR Data: DP1.30003.001 https://data.neonscience.org/data-products/DP1.30003.001
- Breeding landbird point counts DP1.10003.001 https://data.neonscience.org/data-products/DP1.10003.001
- AVONET (Tobias et al. 2022): https://figshare.com/s/b990722d72a26b5bfead
- EltonTraits 1.0 databases (Wilman et al. 2014): https://doi.org/10.6084/m9.figshare.c.3306933.v1
- Daymet (Thornton et al. 2022): https://daymet.ornl.gov/getdata
- Species range maps: BirdLife International https://datazone.birdlife.org/species/requestdis
- Phylogenetic Trees: Bird Tree (Jetz et al. 2012) - Ericson backbone: https://birdtree.org/downloads/
Code/Software
This dataset also relied on a number of R scripts that are available on GitHub through the following link:
Data assoiciated with this project came from the following datasets:
- National Ecological Observatory Network (NEON) shapefiles: https://www.neonscience.org/data-samples/data/spatial-data-maps
- LiDAR Data: NEON data product: DP1.30003.001
- Breeding landbird point counts/Elevation/latitude: NEON data product DP1.10003.001
- Trait data: AVONET (Tobias et al. 2022) and EltonTraits 1.0 databases (Wilman et al. 2014).
- Temperature Range: Daymet (Thornton et al. 2022)
- Species range maps: BirdLife International (BirdLife International 2022)
- Phylogenetic Trees: Bird Tree (Jetz et al. 2012) - Ericson backbone
Data were obtained using R packages (such as neonUtlites) or otherwise downloading existing datasets from publicly availible data repositories. We used data from 385 avian plots from 38 NEON terrestrial sites across 17 of the 20 NEON Domains. 260 species were included across all avian plots. Data came from 2017. Plots were 250m in radius.
We processed the LiDAR data using the lidR package, creating 11 derived structural metrics from LiDAR pointcloud data based on 0.5m x 0.5m x 0.5m voxels derived form height normalized pointclouds. Breeding landbird point counts were corrected for incomplete detection using distance sampling methods, using species range maps to further refine model outputs. Functional, phylogenetic, and PCoA axes were also calculated using trait and phylogenetic datasets.
