Code from: The relative influence of climate extremes and species richness on the temporal variability of bird communities
Data files
Jan 10, 2025 version files 89.35 KB
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R_Code_Cady_etAl_Community_Stability2024.R
16.39 KB
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README.md
2.91 KB
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SpeciesList.csv
70.05 KB
Abstract
Understanding the relationship between biodiversity and ecological stability is increasingly urgent as rapid species extinction continues. Though evidence of positive diversity-stability relationships is accumulating, empirical results are inconsistent and effect sizes tend to be small, raising questions about relative contributions of intrinsic (i.e., species composition/interactions) and extrinsic (i.e., environmental) drivers of stability. Community stability may be more strongly influenced by environmental conditions than by community diversity in some contexts, yet little is known about the comparative importance of diversity and climate means, extremes, and variability in regulating stability. We used a half-century of continental-scale bird data to quantify avian community temporal variability (a metric often used to approximate ecological stability) at 1,379 sites and compared relative effects of climatic variables and species richness. We found that extreme heat and extremely low precipitation at decadal scales are associated with high bird community variability and these climate variables outperformed species richness in terms of variance explained and magnitude of effect. This provides empirical support for the theoretical concept that, at a continental, decadal scale, environmental conditions can play a larger role than intrinsic factors in determining community stability. Our findings also increase understanding of how climate extremes cause diverse ecological responses.
README: Code from: The relative influence of climate extremes and species richness on the temporal variability of bird communities
Date: Mar 30, 2023
Lead author contact: Samantha M. Cady, University of Nebraska-Lincoln (samantha.cady@unl.edu)
Additional authors/cooperators: Samuel D. Fuhlendorf (Oklahoma State University), Craig A. Davis (Oklahoma State University), Barney Luttbeg (Oklahoma State University), Caleb P. Roberts (University of Arkansas), and Scott R. Loss (Oklahoma State University)
DATA
User must download 5 open-source datasets and 1 dataset from Cady et al. (2023) on Dryad before running the accompanying R Code.
Open Source Data:
Datasets 1-3: Breeding Bird Survey 2019 Release, state-level data 1966-2018, weather.csv, and coords.csv. All three datasets are available online:
Pardieck, K.L., Ziolkowski, D.J., Lutmerding, M., Aponte, V.I. & Hudson, M.-A.R. (2019). North American Breeding Bird Survey Dataset 1966-2018 (ver. 2018.0). Accessed Aug, 2019 from https://www.pwrc.usgs.gov/bbs/ (North America Breeding Bird Survey data)
Dataset 4: US EPA Level III ecoregions. Open-source shapefile available at:
https://www.epa.gov/eco-research/level-iii-and-iv-ecoregions-continental-united-states
Dataset 5: PRISM climate--Climate data extracted from PRISM rasterized data. Raw PRISM data are publicly available at: https://prism.oregonstate.edu/ Each row should be a BBS route ID and each column monthly data for precip, tmed, tmax, and tmin extracted at each BBS route start point for temporal extent of study (1967-2018).
PRISM Climate Group, Oregon State University. (2018). Accessed Aug, 2019 from https://prism.oregonstate.edu/ (climate data)
Metadata:
Points.RTENO= unique BBS route identifier
Columns 2:2497= weather variables (maximum temperature, mean temperature, minimum temperature, total precipitation) for each month and year between 1967-2018. Naming convention retained from PRISM rasters
Manuscript-specific Data:
Dataset 6: SpeciesList.csv --dataframe available on Dryad to inform which species to exclude from analysis (waterbirds, raptors, etc.)
Metadata:
AOU=original AOU code for bird species;
AOU2=new AOU code for lumped subspecies (i.e., all subspecies given the same AOU code under AOU2);
Columns 3:5 and 8:11 are species taxonomic information;
Unid= binary value: if 1 species ID was uncertain and species was removed if 0 ID observaton was highly confident and species was retained;
Remove= binary value: if 1 species was removed if 0 species was retained
CODE
Source code format: R
Filename: R_Code_Cady_etAl_Community_Stability2024.R
Dependencies: tidyverse; sp; raster; rgdal; lme4; bbmle; reshape2; stringr; vegan