DOI: 10.5061/dryad.j0zpc86mg
title: Data from: Species-specific ecological traits, phylogeny, and geography underpin vulnerability to population declines for North American birds

description: Species declines and extinctions characterize the Anthropocene.
 Determining species vulnerability to decline, and where and how to
 mitigate threats, are paramount for effective conservation. We
 hypothesized that species with shared ecological traits also share
 threats, and therefore may experience similar population trends. Here, we
 used a Bayesian modeling framework to test whether phylogeny, geography,
 and 22 ecological traits predict regional population trends for 380 North
 American bird species. Groups like blackbirds, warblers, and shorebirds,
 as well as species occupying Bird Conservation Regions at more extreme
 latitudes in North America, exhibited negative population trends, while
 groups such as ducks, raptors, and waders, as well as species occupying
 more inland Bird Conservation Regions, exhibited positive trends.
 Specifically, we found that in addition to phylogeny and breeding
 geography, multiple ecological traits contributed to explaining variation
 in regional population trends for North American birds. Furthermore, we
 found that regional trends and the relative effects of migration distance,
 phylogeny, and geography differ between shorebirds, songbirds, and
 waterbirds. Our work provides evidence that multiple ecological traits
 correlate with North American bird population trends, but that the
 individual effects of these ecological traits in predicting population
 trends often vary between different groups of birds. Moreover, our results
 reinforce the notion that variation in avian population trends is
 controlled by more than phylogeny and geography, where closely-related
 species within one region can show unique population trends due to
 differences in their ecological traits. We recommend that regional
 conservation plans, i.e. one-size-fits-all plans, be implemented only for
 bird groups with population trends under strong phylogenetic or geographic
 controls. We underscore the need to develop species-specific research and
 management strategies for other groups, like songbirds, that exhibit high
 variation in their population trends and are influenced by multiple
 ecological traits.
description: For more detail refer the associated manuscript.
description: Applications that are needed: R and RStudio.
description: This README file was generated on 2023-09-07 by Henry C. Stevens. #
 General Information 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
 &gt; IOC &gt; 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 4. Links/relationships to ancillary data sets: None 5. Was
 data derived from another source? Yes -- data files uploaded to Zenodo 6.
 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. &gt; Written with
 [StackEdit](https://stackedit.io/).