This README file was generated on 2023-09-07 by Henry C. Stevens.

1. Title: Dataset for manuscript "Species-specific ecological traits, phylogeny, and geography underpin vulnerability to population declines for North American birds"
2. Corresponding author: Henry C. Stevens, Georgetown University henrycstevens@gmail.com
3. Basic description:
   This dataset contains all of the data and code necessary to reproduce the analyses in the Ornithological Applications article "Species-specific ecological traits, phylogeny, and geography underpin vulnerability to population declines for North American birds". Each data file associates North American bird species and some number of their relevant ecological traits. Combined, these data files act as the master trait dataset that we analyze and model for the manuscript.

Data overview

Data file list:

1. ACAD.csv
2. BBS_BCR_shrunken_trends.csv
3. bird_diets.csv
4. migration-distance.csv
5. newtrends.csv
6. synonymy.csv
7. utah_birdbase.csv

*NOTE: Some of these data files do not comply with the CC0 license waiver and thus are all uploaded as supplementary information.

Model object list:

1. 2023brm_LpLbmIiHDCaFIDmFl.rds
2. brm_ordermodel_Charadriiformes_migration_20000it.rds
3. brm_ordermodel_migration_10000it.rds
4. brm_ordermodel_Passeriformes_migration_20000it.rds
5. brm_ordermodel_Pelecaniformes_migration_20000it.rds

Other files list:

1. BCR_Terrestrial_master.shp
2. ORNITH-APP-23-003_R_script.R
3. output.nex
4. output2.nex

In all data files, cells with missing values are labeled with "NA".

DATA-SPECIFIC INFORMATION FOR: ACAD.csv

1. Number of variables: 71
2. Number of cases/rows: 1605
3. Variable List: This data file is a copy of the Avian Conservation Assessment Database. This database, and detailed metadata, are publicly available at this link (https://pif.birdconservancy.org/avian-conservation-assessment-database/)

DATA-SPECIFIC INFORMATION FOR:
BBS_BCR_shrunken_trends.csv

1. Number of variables: 10
2. Number of cases/rows: 5926
3. Variable list:

• Species.Name: Common name of bird species
• AOU: American Ornithological Union taxonomic checklist species ID number
• Region: Code for Bird Conservation Region
• Region.Name: Descriptive name for each Bird Conservation Region
• shrunk_trend: Population trend estimate for one species in one Bird Conservation Region based on Breeding Bird Survey data from 1970-2017 shrunk towards the overall mean for the given Bird Conservation Region
• shrunk_trend_lci: lower bounds of 95% confidence interval for shrunk trend estimate
• shrunk_trend_uci: upper bounds of 95% confidence interval for shrunk trend estimate
• Original_Trend: original population trend estimate for one species in one Bird Conservation Region before shrinking towards the overall mean of the given Bird Conservation Region
• Original_Trend_lci: lower bounds of 95% confidence interval for original trend estimate
• Original_Trend_uci: upper bounds of 95% confidence interval for original trend estimate

DATA-SPECIFIC INFORMATION FOR:
bird_diets.csv

1. Number of variables: 6
2. Number of cases/rows: 530
3. Variable list:
   • species: Common name of bird species
   • sci_name: Scientific name of bird species
   • insect_importance: Coarse estimate of how much a given species relies on insects throughout its annual cycle (1 = low importance, 10 = entirely dependent on insects). Score only based on major diet classifications from species accounts.
   • Insect.importance.detail: Detailed estimate of how much a given species relies on insects throughout its annual cycle (1 = low importance, 10 = entirely dependent on insects). Score based on mixed of expert opinion, literature, and detailed species accounts.
   • other food sources: Other known food sources beyond insects
   • allaboutbirds.org & Audubon: Further details on species diet available from AllAboutBirds and Audubon Society species accounts.

DATA-SPECIFIC INFORMATION FOR:
migration-distance.csv

1. Number of variables: 10
2. Number of cases/rows: 11146
3. Variable list:

• species: Scientific name for bird species
• lon.b: Longitudinal coordinate of centroid of breeding range
• lat.b: Latitudinal coordinate of centroid of breeding range
• lon.w: Longitudinal coordinate of centroid of wintering range
• lat.w: Latitudinal coordinate of centroid of wintering range
• Dst.migrated.km: Average annual distance migrated (measured in kilometers) for each species calculated by estimating the great circle distance between the breeding and wintering range centroids.
• Area.b: Total breeding range area in square kilometers
• Area.w: Total wintering range area in square kilometers
• Area.r: Total area in square kilometers where species is considered resident
• Area.p: Total area in square kilometers where species moves through but is not considered resident (i.e., passage)

DATA-SPECIFIC INFORMATION FOR:
newtrends.csv
Note: These data are not used as part of the analysis from the Ornithological Applications manuscript. These data are included if users which to repeat the Ornithological Applications analysis using only global trend data.

1. Number of variables: 12
2. Number of cases/rows: 47
3. Variable list:

• sp: Unique species ID number assigned by taxonomic order
• new_trend: Population trend estimate for each species based on Breeding Bird Survey data from 1970-2017 shrunk towards the overall means of the given Breeding and Nonbreeding biomes.
• new_trend_lci: Lower bounds of 90% confidence interval for trend estimate
• new_trend_uci: Upper bounds of 90% confidence interval for trend estimate
• CommonName: Common name of bird species
• trendyr: Population trend estimate for each species for current based on Breeding Bird Survey data from 1970-2017 (no shrinkage)
• lcI_90CI: Lower bounds of 90% confidence interval for trend estimate
• ucI_90CI: Upper bounds of 90% confidence interval for trend estimate
• BreedingBiome: Primary breeding biome for each bird species
• NonbreedingBiome: Primary nonbreeding biome for each bird species
• log_trend: "trendyr" log-transformed
• var_trend: Variance of trend estimate

DATA-SPECIFIC INFORMATION FOR:
synonymy.csv

1. Number of variables: 4
2. Number of cases/rows: 9994
3. Variable list:

• JetzTip: Species name according to Jetz et al. (2012) global phylogeny of bird species
• is.in.geo: Does the species name manually entered match the species name according to Jetz et al. (2012)? (TRUE/FALSE)
• geo.name: Species name manually entered
• Family: Taxonomic family of bird species

DATA-SPECIFIC INFORMATION FOR:
utah_birdbase.csv

1. Number of variables: 46
2. Number of cases/rows: 1603
3. Variable list:

• IOC #: International Ornithological Congress checklist species ID number
• Latin (BirdLife > IOC > Clements): scientific name for each bird species. When there are conflicts in taxonomy, use the BirdLife name first, then IOC, then Clements.
• English: common name for each bird species.
• Gill et al 2020. IOC World Bird List (v10.2): scientific name according to IOC
• HBW and BirdLife International (2019): scientific name according to Birds of the World and BirdLife International (as of 2019)
• eBird Clements Checklist v2019: scientific name according to Clements checklist (as of 2019)
• Order: taxonomic order of each species
• Family: taxonomic family of each species
• Genus: taxonomic genus of each species
• species: taxonomic species of each species
• IUCN Red: current status of species on IUCN red list
• Restricted: does species have a restricted range? (1 = yes, 0 = no)
• Country Endemic: is species endemic to a country? (1 = yes, 0 = no)
• ISL: does species occur on islands? (1 = yes, 0 = no)
• Average Body Mass: average body mass across entire species in grams
• Primary Habitat: primary habitat association of species across annual cycle
• HB: habitat breadth (score +1 for each major habitat type used during annual cycle)
• Birdlife Forest Dependency: how much does species rely on habitat designated by BirdLife International?
• DB: dietary breadth (score +1 for each major habitat type used during annual cycle)
• Primary Diet: primary dietary association of species across annual cycle
• Foraging Layer: average foraging layer for species within elevational structure of its preferred habitat type (G = ground, W = water, C = canopy, H = high elevation, M = mid elevation, L = low elevation, U = understory)
• Carn sum: total major carnivorous components of diet (e.g., fish + rodents = 2)
• Herb sum: total major herbivorous components of diet (e.g., seeds + fruit = 2)
• Nest: type of nest (e.g., CP = cup)
• SBS: nesting substrate (e.g., G = ground)
• Clutch.Min: average minimum clutch size (# of eggs)
• Clutch Max: average maximum clutch size (# of eggs)
• Clutch.Ave: average total clutch size (# of eggs)
• Inc1: lower estimate of average incubation time (days) for one nest attempt
• Inc2: upper estimate of average incubation time (days) for one nest attempt
• Fledge: average time (days) until young fledge from a nesting attempt
• Known Bird Annual Survival: known estimate of annual survival for bird species based on data from the Institute for Bird Populations
• Known Bird Age at First Breeding: known estimate of age at first breeding for bird species based on data from the Institute for Bird Populations
• Known Bird Longevity: known estimate of longevity for bird species based on data from the Institute for Bird Populations
• Modelled Bird Annual Survival: modeled estimate of annual survival for bird species based on data from the Institute for Bird Populations
• Modelled Bird Age at First Breeding: modeled estimate of age at first breeding for bird species based on data from the Institute for Bird Populations
• Modelled Bird Longevity: modeled estimate of bird longevity for bird species based on data from the Institute for Bird Populations
• Modelled Bird GenLength: modeled estimate of generation length for bird species based on data from the Institute for Bird Populations

MODEL-SPECIFIC INFORMATION

Each of the listed model objects correspond to Bayesian models analyzed and discussed in the Ornithological Applications manuscript.

A. "2023brm_LpLbmIiHDCaFIDmFl.rds": the top-performing global ecological trait model comprising the first analysis in the manuscript

B. "brm_ordermodel_Charadriiformes_migration_20000it.rds", "brm_ordermodel_Passeriformes_migration_20000it.rds",
"brm_ordermodel_Pelecaniformes_migration_20000it.rds": these three models correspond with the order-specific analysis in the manuscript where the relative influence of phylogeny, geography, and migration distance are unique between shorebirds, songbirds, and waterbirds.

C. "brm_ordermodel_migration_10000it.rds": finally, this model corresponds with the global random-slopes model for exploring how the role of one ecological trait changes between different bird orders.

INFORMATION ON OTHER FILES:

1. BCR_Terrestrial_master.shp Shapefile of the Bird Conservation Region boundaries in North America.
2. ORNITH-APP-23-003_R_script.R: R script for conducting all data preparation, manipulation, and analysis associated with the Ornithological Applications manuscript.
3. output.nex Phylogenetic tree for North American birds created using the Jetz et al. (2012) global bird phylogeny. Use this tree when analyzing the global species trends.
4. output2.nex Phylogenetic tree for North American birds created using the Jetz et al. (2012) global bird phylogeny. Use this tree when analyzing the Bird Conservation Region species trends.

Sharing/Access information

1. Licenses/restrictions placed on the data: For files uploaded in Dryad: CC0 1.0 Universal (CC0 1.0) Public Domain For files uploaded in Zenodo: CC-BY
2. Links to publications that cite or use the data:

Stevens, H. C., A. C. Smith, E. R. Buechley, Ç. H. Şekercioğlu, V. M. Shirey, K. V. Rosenberg, F. A. La Sorte, D. Tallamy, and P. P. Marra (2023). Species-specific ecological traits, phylogeny, and geography underpin vulnerability to population declines for North American birds. Ornithological Applications. doi: 10.1093/ornithapp/duad046

Links to other publicly accessible locations of the data:
Most data archived here are from unpublished datasets. Only one, the Avian Conservation Assessment Database, is publicly available:

Link: https://pif.birdconservancy.org/avian-conservation-assessment-database/

Other datasets archived here were derived from the following institutions:

• Insect dependence scores -- D. Tallamy at the University of Delaware
• Global trait database -- C. Sekercioglu at the University of Utah
• Migration distance dataset -- F. La Sorte at the Cornell Lab of Ornithology

1. Links/relationships to ancillary data sets: None
2. Was data derived from another source? Yes -- data files uploaded to Zenodo
3. Recommended citation for this dataset:

Stevens, H. C., A. C. Smith, E. R. Buechley, Ç. H. Şekercioğlu, V. M. Shirey, K. V. Rosenberg, F. A. La Sorte, D. Tallamy, and P. P. Marra (2023). Dataset for manuscript: Species-specific ecological traits, phylogeny, and geography underpin vulnerability to population declines for North American birds. Dryad Digital Repository. doi:10.5061/dryad.j0zpc86mg

Code/Software

The R script "ORNITH-APP-23-003_R_script" contains all of the R code necessary to reproduce the analyses in the associated manuscript. We strongly recommend running the script in RStudio.

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