AVOTREX: A global dataset of extinct birds and their traits (v. 1.0)

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.

Methods
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.