These data can be used to recreate analyses in the paper: The global loss of avian functional and phylogenetic diversity from anthropogenic extinctions. For easier use, it is recommended to download the repo as a whole from GitHub (txm676/GlobalFDPDLoss); doing this and setting the working directory within R to the main repo directory should then allow all the scripts to run through.

All analyses were run in R.

Description of the data and file structure

allSp_phylo.csv

Island endemism status, IUCN Red List classification, generation length and extinction status information
for all species (extant and extinct), following the BirdTree taxonomy.

species = Binomial name (BirdTree taxonomy)
species_BirdLife = Birdlife binomial name
Extant = Lists the species as either extant or extinct.
ExtinctionPeriod = Groups the species as either Current, EX_Other or EX_IUCN:
*Current = extant species
*EX_IUCN = species classified as extinct by the IUCN
*EX_Other = all other extinct species
ExtinctionType = Groups the species as either Current, EX_A, EX_U, EX_IUCN:
*EX_U = Non-IUCN extinctions of unknown cause
*EX_A = Non-IUCN anthropogenic extinctions.
*IUCN = species classified as extinct by the IUCN (all anthropogenic)
IslandEndemic = Identifies if the species is an island endemic. Binary (Yes/No).
IUCN = IUCN red list designation. One of LC (least concern), NT (near threatened), VU (vulnerable), EN (endangered), CR (critically endangered), or DD (data deficient).
GenLength = Generation length.
IslandEndemic2 = island endemism status based on the seabird sensitivity analysis.

AVONET_BIRDLIFE.csv

Trait data for extant species from the published AVONET dataset, following the Birdlife taxonomy.

species = Binomial name (BirdTree taxonomy)
Genus = Genus
Family = Family
Order = Order
Beak.Length_Culmen = Length from the tip of the beak to the base of the skull (mm)
Beak.Length_Nares = Length from the anterior edge of the nostrils to the tip of the beak (mm)
Beak.Width = Width of the beak at the anterior edge of the nostrils (mm)
Beak.Depth = Depth of the beak at the anterior edge of the nostrils (mm)
Tarsus.Length = Length of the tarsus from the posterior notch between tibia and tarsus, to the end of the last scale of acrotarsium (at the bend of the foot) (mm)
Wing.Length = Length from the carpal joint (bend of the wing) to the tip of the longest primary on the unflattened wing (mm)
Kipps.Distance = Length from the tip of the first secondary feather to the tip of the longest primary (mm)
Secondary1 = Length from the carpal joint (bend of the wing) to the tip of the first secondary, i.e. the outermost secondary adjacent to the innermost primary feather. Secondary1 is roughly equivalent to Wing length minus Kipp’s distance (measured in a fully folded and flat wing) (mm)
Hand-Wing.Index = 100*DK/Lw, where DK is Kipp’s distance and Lw is wing length (i.e., Kipp’s distance corrected for wing size).
Tail.Length = Distance between the tip of the longest rectrix and the point at which the two central rectrices protrude from the skin, typically measured using a ruler inserted between the two central rectrices (mm)
Mass = Body mass given as species average (incorporating both male and female body mass) (g)
Mass.Source = Source of mass data
Inference = Whether or not mass data were inferred
Habitat = Primary species habitat classification
Trophic.Level = Primary species trophic level classification
Trophic.Niche = Primary species trophic niche classification
Primary.Lifestyle = Primary species lifestyle classification

See Tobias et al. (2022) for further details:
Tobias, J. A., Sheard, C., Pigot, A. L., Devenish, A. J., Yang, J., Sayol, F., ... & Schleuning, M. (2022). AVONET: morphological, ecological and geographical data for all birds. Ecology Letters, 25(3), 581-597.

ExtinctImputedTraits_Averages.csv

Trait data for extinct species, as well as island endemic classifications, extinction time period and
location data, for all extinct species.
species = Binomial name (roughly following BirdLife taxonom)
Genus = Genus
Family = Family
Order = Order
Jetz_Order = Order following the BirdTree taxonomy. Format is all capitilised.
Jetz_Family = Family following the BirdTree taxonomy.
Jetz_Genus = Genus following the BirdTree taxonomy.
Beak.Length_Culmen, Beak.Length_Nares, Beak.Width, Beak.Depth, Tarsus.Length, Wing.Length, Kipps.Distance,
Tail.Length (all mm), and Mass (g) match the traits in AVONET for extinct species (see above).
ExtinctionType = As for the allSp_phylo dataset (described above), with the addition of:
EW = extinct in the wild
ExtinctionPeriod = As for the allSp_phylo dataset (described above), with the addition of EW.
ExtinctionPeriodMAP = The same as ExtinctionPeriod but has an extra category (EX_POST1500) for the 19 EX_Other species that are post-1500
extinctions but not currently recognised by the IUCN. Is just used to make the map in Figure 1.
IslandEndemic = As for the allSp_phylo dataset.
Isl_group_map = Groups the species into island groups or continental groups for mapping (i.e., Figure 1).
LAT = Latitude of the island or continental group.
LON = Longitude of the island or continental group.
Isl_group_map2 = Either NA, i.e., the species is present on no other continental or island group, or groups the species into a second group.
LAT2 = If applicable, the latitude of the second island or continental group.
LON2 = If applicable, the latitude of the second island or continental group.
Isl_group_map3 = Either NA, i.e., the species is present on only one or two continental or island group(s), or groups the species into a third group.
LAT3 = If applicable, the latitude of the third island or continental group.
LON3 = If applicable, the latitude of the third island or continental group.

dendro_all.R (.RData file)

The dendrogram (built using neighbour joining) with all extant and extinct species (Birdlife taxonomy). An object of class 'phylo'.

future.rds

The future extinction simulation data (.rds). A list with six elements (each corresponding to a specific taxonomy and species subset), each a list of
100 elements (from 100 individual simulations) storing the extant species names selected to go extinct:
[1] "Birdlife_all" "Birdlife_isl"
[3] "Birdtree_all" "Birdtree_isl"
[5] "Birdlife_isl2" "Birdtree_isl2"
all = global avifauna analyses; isl = island endemic analyses; isl2 = seabird sensitivity analyses
Birdlife = Birdlife taxonomy; Birdtree = BirdTree taxonomy

JetzExtinct50Trees.rds

A list of 50 phylogenies (each of class 'avophylo' and 'phylo'), each containing all of the currently extant species (BirdTree taxonomy) and the extinct species grafted on.

Master_phylo_spreadsheet_V17.xlsx

The spreadsheet which is used within the avotrex R package to graft all extinct species onto
the BirdTree phylogenies. Also supplied as a data object within the package.
Grafting codes are located in the Type column, and code information is provided in the Supp info.

Id_sps = The extinct species ID.
phylo_id2 = The phylo ID. This is used for the grafting order.
per_fixed = logical value stating whether or not a species should be grafted at a fixed point along a branch rather than random.
time_fixed = time point (in Myrs) for grafting specific species at specific time points on the tree.
Group = Either NA, or the group the extinct species is placed within. Species within groups are then randomised before grafting.
species = Species name. Format requires an underscore to separate the genus and the species name.
Genus = Genus
Family = Family
Order = Order
Jetz_Order = Order following the BirdTree taxonomy. Format is all capitilised.
Jetz_Family = Family following the BirdTree taxonomy
Jetz_Genus = Genus following the BirdTree taxonomy
Type = The type of join required for the extinct species. See table below for details on each code.
Sister_order = Either NA, or the name of the sister order(s) that the extinct species needs to be joined to or placed within.
Sister_clade = Either NA, or the name of the sister clade(s) that the extinct species needs to be joined to or placed within.
Sister_family = Either NA, or the name of the sister family(s) that the extinct species needs to be joined to or placed within.
Sister_genus = Either NA, or the name of the sister genus or genera that the extinct species needs to be joined to or placed within.
Sister_species = Either NA, or the name of the sister species that the extinct species needs to be joined to. Genus must also be supplied.
Sister_species_group = Either NA, or the names of multiple sister species that the extinct species needs to be randomly grafted to. Species must be separated with a semi-colon,
and the genus and species name (for an individual species) must be separated with an underscore.

allSp_birdlife.csv 

Island endemism, generation length and IUCN Red list status data for all extant species following the
Birdlife taxonomy.
Order = Order according to the Birdlife taxonomy.
Family = Family according to the Birdlife taxonomy.
Genus = Genus according to the Birdlife taxonomy
species = Species name according to the Birdlife taxonomy.
status = IUCN red list status, one of LC (least concern), NT (near threatened), VU (vulnerable), EN (endangered), CR (critically endangered), or DD (data deficient).
IslandEndemic = Identifies if the species is an island endemic. Binary (Yes/No).
GenLength = Generation length.
IslandEndemic2 = island endemism status based on the seabird sensitivity analysis.