DOI: 10.5061/dryad.12jm63z44
title: The global loss of avian functional and phylogenetic diversity from anthropogenic extinctions

description: Humans have been driving a global erosion of species richness for
 millennia, but the consequences of past extinctions for other dimensions
 of biodiversity – functional and phylogenetic diversity – are poorly
 known. Here, we show that, since the Late Pleistocene, the extinction of
 610 bird species has caused a disproportionate loss of the global avian
 functional space along with ~3 billion years of unique evolutionary
 history. For island endemics, proportional losses have been even greater.
 Projected future extinctions of more than 1000 species over the next two
 centuries will incur further substantial reductions in functional and
 phylogenetic diversity. These results highlight the severe consequences of
 the ongoing biodiversity crisis and the urgent need to identify the
 ecological functions being lost through extinction.
description: # The global loss of avian functional and phylogenetic diversity from
 anthropogenic extinctions 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. | Codes | Full name | Definition | | ----- |
 --------------------------- |
 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | S | Sister | Grafted as a sister to a known extant or extinct species already in the tree | | SSG | Sister species group | Grafted as a sister to a group of extant and/or extinct species already in the tree | | SGG | Sister genus group | Grafted as a sister to an entire extant or extinct genus (i.e., for the first grafted representative of an extinct genus) | | SGG2 | Sister genus group 2 | Grafted as sister to multiple genera. This was for when a species was sister to a subfamily or some other large specific clade | | SFG | Sister family group | Grafted as a sister to an entire extant or extinct family already present in the tree (i.e., for the first grafted representative of an extinct family) | | SOG | Sister order group | Grafted as a sister to an entire order already present in the tree (i.e., for the first grafted representative of an extinct order) | | RSG | Random species group | Grafted to a randomly selected species from a pre-defined group of species (i.e., from which is believed to have close affinities | | RGG | Random genus group | Grafted to a randomly selected species from a given genus. For example, if an extinct species was believed to be a finch derived from a European finch species, but the exact sister species is unknown. | | RGG2 | Random genus group 2 | Grafted to a randomly selected species from a group of genera (e.g. when all that is known is that the species is from a specific subfamily). Currently not used in the database, but the relevant functionality has been kept in the R script, as it could be useful for future studies. | | RFG | Random family group | Grafted to a randomly selected species from a given family | | RSGG | Random sister genus group | Grafted as sister to a randomly selected genus from a pre-defined group of genera | | RSGG2 | Random sister genus group 2 | Grafted as sister to a randomly selected genus from a pre-defined family | ### 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.