DOI: 10.5061/dryad.zgmsbcckk
title: AVOTREX: A global dataset of extinct birds and their traits (v. 1.0)

description: Human activities have been reshaping the natural world for tens of
 thousands of years, leading to the extinction of hundreds of bird species.
 Past research has provided evidence of extinction selectivity towards
 certain groups of species, but trait information is lacking for the
 majority of clades, especially for prehistoric extinctions identified only
 through subfossil remains. This incomplete knowledge potentially obscures
 the structure of natural communities, undermining our ability to infer
 changes in biodiversity across space and time. Biases in currently
 available trait data also limit our ability to identify drivers and
 processes of extinction. Here we present AVOTREX, an open-access database
 of species traits for all birds known to have gone extinct in the last
 130,000 years. This database provides detailed morphological information
 for 610 extinct species. For each extinct bird species, we provide
 information on the taxonomy, geographic location, and period of
 extinction. We also present data on island endemicity, flight ability and
 body mass, as well as standard measurements of external (matching the
 AVONET database of extant birds) and skeletal morphology from museum
 specimens where available. To ensure comprehensive morphological data
 coverage, we estimate all missing morphological measurements using a data
 imputation technique based on machine learning. This method can integrate
 measurements from different sources (i.e. skeletal and skin material),
 together with taxonomic information, and allows us to provide complete
 information on standard morphological traits of all known extinct birds.
description: The AVOTREX dataset includes information on eight external
 morphological measurements (in mm) commonly used in the avian literature,
 all of which are included in the AVONET database. These comprise four beak
 measurements (depth, width, length from culmen, and length from nares),
 two wing measurements (total wing chord length and Kipp’s distance [length
 from the tip of the first secondary feather to the tip of the longest
 primary]), tarsus length and tail length. The external morphological
 measurements were taken from preserved skins of specimens in natural
 history collections or from literature sources. We also obtained body mass
 (g) for extinct birds from the literature. Any missing data on external
 morphological measurements (i.e., because only subfossil or skeletal
 remains exist) were imputed. To inform the imputation process, we also
 included skeletal measurements. To this end, we collected data for 22
 linear skeletal measurements from museum specimens and the literature. The
 skeletal measurements include the same four beak measurements (depth,
 width length from culmen, and length from nares), and three measures for
 the hindlimbs and forelimbs (total length, proximal width, and distal
 width for each bone). Our dataset also included information on body mass
 and flight ability from the literature. All missing data was imputed using
 a Bayesian Hierarchical Probabilistic Matrix Factorization (BHPMF)
 approach. This method uses a machine learning algorithm to impute missing
 entries within a species trait matrix and can incorporate hierarchical
 taxonomic information to guide the imputation.
description: # AVOTREX: a global dataset of extinct birds and their traits (v. 1.0)
 **Authors:** Ferran Sayol, Joseph P. Wayman, Paul Dufour, Thomas E.
 Martin, Julian P. Hume, Maria Wagner Jørgensen, Natàlia Martínez-Rubio,
 Ariadna Sanglas, Filipa C. Soares, Rob Cooke, Chase D. Mendenhall, Jay R.
 Margolis, Juan Carlos Illera, Rhys Lemoine, Eva Benavides, Oriol Lapiedra,
 Kostas A. Triantis, Alex L. Pigot, Joseph A. Tobias, Søren Faurby &
 Thomas J. Matthews. Comments and requests should be addressed to Ferran
 Sayol: [fsayol@gmail.com](mailto:fsayol@gmail.com). ### Description of the
 data and file structure: Avotrex_metadata.xlsx : Spreadsheet file
 containing the definitions of all variables (with their corresponding
 units), abbreviations, and acronyms used within the dataset files. The
 document comprises the following sheets: * Metadata_Avotrex: Description
 of variables from AVOTREX (v. 1.0) files * Metadata_Avonet: Description of
 variables from AVONET database * Metadata_RawData_D1-D8: Description of
 variables from RawData_D1-D8 * Ref_IDs: List of reference IDs used within
 the AVOTREX dataset files and their corresponding full references from
 which the information for the species in the database was extracted. Short
 codes were created using the following formula: 'first author
 surname' + underscore + 'year of publication'. *
 Collection_IDs: List of collection ID acronyms and their corresponding
 full name, city, and location, from which the specimens measured for the
 AVOTREX database belong. * Measurer_IDs: List of unique identifiers
 (initials or other abbreviation) and their corresponding full names, used
 to identify each individual measurer within the AVOTREX database.
 Avotrex_taxonomy_v1.csv : Taxonomy of the 610 species that are part of the
 AVOTREX database. Avotrex_traits_v1.csv : Status, distribution and
 external morphological measurements, either measured or imputed, of the
 610 species that are part of the AVOTREX database. DB_Avonet_BirdLife.csv
 : Contains the external morphological measurements of 11009 extant bird
 species from the Avonet database. For more information see Tobias et al
 2022 Ecology Letters DOI:
 [https://doi.org/10.111/ele.13898](https://doi.org/10.111/ele.13898)
 RawData_D1.csv : External morphological measurements for extinct species
 taken from preserved skins of specimens in natural history collections.
 RawData_D2.csv : External morphological measurements for extinct species
 from preserved skins of specimens gathered from literature sources.
 RawData_D3.csv : Skeletal measurements for extinct species taken from
 museum specimens. RawData_D4.csv : Skeletal measurements for extinct
 species gathered from literature sources. RawData_D5.csv : Body mass for
 extinct species gathered from literature sources. RawData_D6.csv :
 Inferred body mass for extinct species based either on qualitative
 descriptions in the literature (i.e., reported to be a similar size to a
 specific close relative) or skeletal proportions (i.e., 10% larger than a
 relative based on femur measurements). RawData_D7.csv : Skeletal
 measurements for extant species taken from museum specimens.
 RawData_D8.csv : Skeletal measurements for extant species gathered from
 literature sources. ### Version changes: **26-oct-2024:** First
 publication of the dataset. **Jan-2025:** Removed `specimen_id` from
 several items in the CM collection in RawData_D3 and RawData_D7 due to
 errors. ### User notes: Across all the spreadsheet files, any cells
 containing "NA" indicate that data is not available for that
 particular trait or variable. The datasets included in this repository are
 part of the AVOTREX (v. 1.0) database. If you find any errors, you can
 report them here to help update future versions of
 AVOTREX: [https://forms.gle/HWPoAri1gyNzBENt8](https://forms.gle/HWPoAri1gyNzBENt8) ### Sharing/Access information: Full reference: Sayol, F., Wayman, J., Dufour, P., Martin, T.E., Hume, J.P., Jørgensen, M., Martínez-Rubio, N., Sanglas, A., Soares, F.C., Cooke, R., Mendenhall, C.D., Margolis, J.R.,Illera, J.C., Lemoine, R., Benavides, E., Lapiedra, O., Triantis, K.A., Pigot, A.L., Tobias, J.A., Faurby, S. & Matthews, T. J. (2024). AVOTREX: a global dataset of extinct birds and their traits. *Global Ecology and Biogeography,* e13927. [https://doi.org/10.1111/geb.13927](https://doi.org/10.1111/geb.13927)