DOI: 10.5061/dryad.v41ns1s4c
title: Skeletal traits for thousands of bird species v1.0

description: The dataset spans 2,057 species of birds (Aves: Passeriformes) and
 includes linear measurements of 12 skeletal elements from 14,419
 individuals. In addition to the trait values directly measured from
 photographs, we leverage the multi-dimensional nature of our dataset and
 known phylogenetic relationships of the species to impute missing data
 under an evolutionary model. The traits included in the dataset are: the
 lengths of the tibiotarsus, humerus, tarsometatarsus, ulna, radius, keel,
 carpometacarpus, 2nd digit 1st phalanx, furcula, and femur; the maximum
 outer diameter of the sclerotic ring, and the length from the back of the
 skull to the tip of the bill (treating the rhamphotheca as part of the
 bill when it remains present on the specimen). These data are presented in
 three ways: 1) a dataset that only includes trait estimates for elements
 that were confidently identified and measured, 2) a complete
 specimen-level dataset that includes imputed trait values for all missing
 data, and 3) a species-mean dataset based on a model of trait evolution
 that includes estimates of the species mean, species-level standard error,
 variance, and 95% confidence interval of the trait estimates.
description: These data were collected from museum skeletal specimens. To
 measure traits, images were taken of skeletal specimens and then
 Skelevision, a computer vision method, was used to segment out the bones
 in the images, identify them, and measure them; this method is described
 in detail in Weeks et al. (2023). In addition to presenting the data that
 were generated using Skelevision, we generated a 100% complete dataset by
 imputing all missing values in the dataset using Rphylopars (Goolsby et
 al. 2017), which is a method for fitting multivariate phylogenetic models
 and estimating missing values in comparative data.  We also present
 species-level means along with associated estimates of uncertainty derived
 from the Rphylopars model. We validated the Skelevision estimates by
 comparing them to handmade measurements, and we assessed the trait
 imputation accuracy by withholding data and imputing the withheld values.
 The validation procedure and results are outlined in detail in Weeks et
 al. (2024).   References: 
 Goolsby, E.W., J. Bruggeman, and C. Ané. 2017. Rphylopars: fast
 multivariate phylogenetic comparative methods for missing data and
 within-species variation. Methods in Ecology and Evolution 8(1):
 22-27. Weeks, B.C., Z. Zhou, B.K. O'Brien, R.
 Darling, M. Dean, T. Dias, G. Hassena, M. Zhang, and D.F. Fouhey. 2023. A
 deep neural network for high-throughput measurement of functional traits
 on museum skeletal specimens. Methods in Ecology and Evolution. 14(2):
 347-359. Weeks, B.C., Z. Zhou, C.M. Probst, J.S. Berve,
 B.K. O'Brien, B.W. Benz, H.R. Skeen, M. Ziebell, L. Bodt, and D.F.
 Fouhey. 2024. Skeletal trait measurements for thousands of bird species.
 bioRxiv. https://doi.org/10.1101/2024.12.19.629481
description: # Skeletal Traits for Thousands of Bird Species v1.0
 [https://doi.org/10.5061/dryad.v41ns1s4c](https://doi.org/10.5061/dryad.v41ns1s4c) ## Description of the data and file structure The data presented here were generated using photographs of museum skeletal specimens. These data were used to generate three versions of the dataset: 1\) Skelevision Only Dataset v1. This version of the dataset only includes traits that were confidently measured using the Skelevision computer vision pipeline, described in detail in Weeks et al. (2023), and implemented as described in Weeks et al. (2024). 2\) Complete Trait Dataset v1. This version of the dataset includes a complete specimen-level dataset. It was generated by imputing all missing trait values using evolutionary models as described and validated in Weeks et al. (2024). 3\) Skelevision species complete v1.1. This version of the dataset presents species mean trait values generated using evolutionary models, as outlined in Weeks et al. (2024) and includes estimates of uncertainty associated with each estimated species mean trait value. References Weeks, B.C., Z., Zhou, B.K. O'Brien, R. Darling, M. Dean, T. Dias, G. Hassena, M. Zhang, and D.F. Fouhey. 2023. A deep neural network for high-throughput measurement of functional traits on museum skeletal specimens. Methods in Ecology and Evolution 14(2): 347-359), and implemented as described in Weeks et al. 2024.  Weeks, B.C., Z. Zhou, C.M. Probst, J.S. Berv, B.K. O'Brien, B.W. Benz, H.R. Skeen, M. Ziebell, L. Bodt, and D.F. Fouhey. Skeletal trait measurements for thousands of bird species. bioRxiv.  ### Files and variables #### File: Skelevision_Only_Dataset_v1.csv **Description:** For skeletal elements that occur in pairs within an individual the measurements presented are either the means of two high quality measures of the element (e.g. if both sclerotic rings were confidently measured, the data for sclerotic ring is the mean of these to measures) or are the single high quality measure made on that specimen. See Weeks et al. (2023) and Weeks et al. (2024) for more detail. ##### Variables * ID: Natural history museum institutional code followed by the specimen catalog number for each row of data. * species: Species binomial for the specimen, following the Birdlife V3 taxonomy. * tarsus: Length of the tibiotarsus in millimeters. * ulna: Length of the ulna in millimeters. * cv.skull.1: Length of the distance from the tip of the bill to the back of the skull in millimeters. * second_digit: Length of the 2nd Digit 1st Phalanx in millimeters. * sclerotic_ring: The longest distance across the outer diameter of the sclerotic ring in millimeters. * metatarsus: Length of the tarsometatarsus in millimeters. * cv.keel.1: Length of the keel in millimeters. * humerus: Length of the humerus in millimeters. * cv.furcula.1: Length of the longest linear dimension of the furcula in millimeters. * femur: Length of the femur in millimeters. * carpometacarpus: Length of the carpometacarpus in millimeters. * radius: Length of the radius in millimeters. #### File: Complete_Trait_Dataset_v1.csv **Description:** A specimen-level dataset not missing any data. The dataset includes both measures directly made with Skelevision and imputed using evolutionary models if direct measurements were not confidently made. For skeletal elements that occur in pairs within an individual the measurements presented are either the means of two high quality measures of the element (e.g. if both sclerotic rings were confidently measured, the data for sclerotic ring is the mean of these to measures) or are the single high quality measure made on that specimen. See Weeks et al. (2023) and Weeks et al. (2024) for more detail. ##### Variables * ID: Natural history museum institutional code followed by the specimen catalog number for each row of data. * species: Species binomial for the specimen, following the Birdlife V3 taxonomy. * tarsus: Length of the tibiotarsus in millimeters. * ulna: Length of the ulna in millimeters. * cv.skull.1: Length of the distance from the tip of the bill to the back of the skull in millimeters. * second_digit: Length of the 2nd Digit 1st Phalanx in millimeters. * sclerotic_ring: The longest distance across the outer diameter of the sclerotic ring in millimeters. * metatarsus: Length of the tarsometatarsus in millimeters. * cv.keel.1: Length of the keel in millimeters. * humerus: Length of the humerus in millimeters. * cv.furcula.1: Length of the longest linear dimension of the furcula in millimeters. * femur: Length of the femur in millimeters. * carpometacarpus: Length of the carpometacarpus in millimeters. * radius: Length of the radius in millimeters. #### File: Skelevision_species_complete_v1.1.csv **Description:** This is a complete species-level dataset that presents mean values for each trait for each species, derived from fitted evolutionary models of trait evolution as outlined in Weeks et al. (2024) along with several estimates of uncertainty.  ##### Variables * Species: Species binomial for the specimen, following the Birdlife V3 taxonomy. * Tarsus: Length of the tibiotarsus in millimeters. * Ulna: Length of the ulna in millimeters. * Skull: Length of the distance from the tip of the bill to the back of the skull in millimeters. * Second_Digit: Length of the 2nd Digit 1st Phalanx in millimeters. * Sclerotic_Ring: The longest distance across the outer diameter of the sclerotic ring in millimeters. * Metatarsus: Length of the tarsometatarsus in millimeters. * Keel: Length of the keel in millimeters. * Humerus: Length of the humerus in millimeters. * Furcula: Length of the longest linear dimension of the furcula in millimeters. * Femur: Length of the femur in millimeters. * Carpometacarpus: Length of the carpometacarpus in millimeters. * Radius: Length of the radius in millimeters. * Tarsus_SE: Estimated standard error in millimeters of the tibiotarsus length. * Ulna_SE: Estimated standard error in millimeters of the ulna length. * Skull_SE: Estimated standard error in millimeters of the skull length. * Second_Digit_SE: Estimated standard error in millimeters of the second digit  length. * Sclerotic_Ring_SE: Estimated standard error in millimeters of the sclerotic ring diameter. * Metatarsus_SE: Estimated standard error in millimeters of the metatarsus length. * Keel_SE: Estimated standard error in millimeters of the keel length. * Humerus_SE: Estimated standard error in millimeters of the humerus length. * Furcula_SE: Estimated standard error in millimeters of the furcula length. * Femur_SE: Estimated standard error in millimeters of the femur length. * Carpometacarpus_SE:  Estimated standard error in millimeters of the carpometacarpus length. * Radius_SE:  Estimated standard error in millimeters of the radius length. * Tarsus_VAR: Estimated variance in millimeters^2 of the tibiotarsus length. * Ulna_VAR: Estimated variance in millimeters^2 of the ulna length. * Skull_VAR: Estimated variance in millimeters^2 of the skull length. * Second_Digit_VAR: Estimated variance in millimeters^2 of the second digit length. * Sclerotic_Ring_VAR: Estimated variance in millimeters^2 of the sclerotic ring diameter. * Metatarsus_VAR: Estimated variance in millimeters^2 of the metatarsus length. * Keel_VAR: Estimated variance in millimeters^2 of the keel length. * Humerus_VAR: Estimated variance in millimeters^2 of the humerus length. * Furcula_VAR: Estimated variance in millimeters^2 of the furcula length. * Femur_VAR: Estimated variance in millimeters^2 of the femur length. * Carpometacarpus_VAR: Estimated variance in millimeters^2 of the carpometacarpus length. * Radius_VAR: Estimated variance in millimeters^2 of the radius length. * Tarsus_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of tibiotarsus length. * Tarsus_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of tibiotarsus length. * Ulna_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of ulna length. * Ulna_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of ulna length. * Skull_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of skull length. * Skull_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of skull length. * Second_Digit_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of second digit length. * Second_Digit_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of second digit length. * Sclerotic_Ring_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of sclerotic ring diameter. * Sclerotic_Ring_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of sclerotic ring diameter. * Metatarsus_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of metatarsus length. * Metatarsus_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of metatarsus length. * Keel_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of keel length. * Keel_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of keel length. * Humerus_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of humerus length. * Humerus_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of humerus length. * Furcula_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of furcula length. * Furcula_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of furcula length. * Femur_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of femur length. * Femur_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of femur length. * Carpometacarpus_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of carpometacarpus length. * Carpometacarpus_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of carpometacarpus length. * Radius_LowerCI: Estimated lower bound in millimeters of the 95% confidence interval of radius length. * Radius_UpperCI: Estimated upper bound in millimeters of the 95% confidence interval of radius length. ## Code/software The datasets are saved as comma separated values (.csv files) and can be viewed in any software that can open this file type.