AVOTREX: A global dataset of extinct birds and their traits (v. 1.0)
Data files
Oct 26, 2024 version files 1.86 MB
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Avotrex_metadata.xlsx
71.71 KB
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Avotrex_taxonomy_v1.csv
76.99 KB
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Avotrex_traits_v1.csv
134.54 KB
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DB_Avonet_BirdLife.csv
1.35 MB
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RawData_D1.csv
23.22 KB
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RawData_D2.csv
2.57 KB
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RawData_D3.csv
19.31 KB
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RawData_D4.csv
49.97 KB
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RawData_D5.csv
2.75 KB
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RawData_D6.csv
4.55 KB
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RawData_D7.csv
72.32 KB
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RawData_D8.csv
53.66 KB
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README.md
4.17 KB
Jan 22, 2025 version files 1.86 MB
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Avotrex_metadata.xlsx
71.71 KB
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Avotrex_taxonomy_v1.csv
76.99 KB
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Avotrex_traits_v1.csv
134.54 KB
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DB_Avonet_BirdLife.csv
1.35 MB
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RawData_D1.csv
23.22 KB
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RawData_D2.csv
2.57 KB
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RawData_D3.csv
19.30 KB
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RawData_D4.csv
49.97 KB
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RawData_D5.csv
2.75 KB
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RawData_D6.csv
4.55 KB
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RawData_D7.csv
71.81 KB
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RawData_D8.csv
53.66 KB
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README.md
4.37 KB
Abstract
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.
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.
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
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
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
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.