This project entailed a data-driven comparison of imputation method performance across 21 different mixed-type trait datasets for amphibians, birds, mammals, fishes, and reptiles. Contained within this repository are the scripts used to perform the analyses and visualize the results, the multiple sequence alignments and phylogenetic trees used for phylogenetic imputation, the error metrics from the imputation runs, and the correlation coefficients from the final imputations.
Trait data for this project were obtained from:
Faurby S, Davis M, Pedersen RØ, Schowanek SD, Antonelli1 A, Svenning J-C. 2020. PHYLACINE 1.2.1: An update to the Phylogenetic Atlas of Mammal Macroecology. doi:10.5281/zenodo.3690867.
Froese R, Pauly D, editors. 2022 Feb. FishBase. World Wide Web Electron Publ. www.fishbase.org.
Jones KE, Bielby J, Cardillo M, Fritz SA, O’Dell J, Orme DL, Safi K, Sechrest W, Boakes E, Carbone C, et al. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology. 90(9):2648.
Meiri S. 2019. Data from: Traits of lizards of the world: Variation around a successful evolutionary design. Dryad Dataset. https://doi.org/10.5061/dryad.f6t39kj.
Oliveira BF, São-Pedro VA, Santos-Barrera G, Penone C, Costa GC. 2017a. AmphiBIO_v1. figshare. https://doi.org/10.6084/m9.figshare.4644424.v5.
Sheard C. 2020 May 18. catherinesheard/Global-HWI v1.1 (Version v1.1). Zenodo. doi:http://doi.org/10.5281/zenodo.3832215.
Wilman H, Belmaker J, Simpson J, de la Rosa C, Rivadeneira MM, Jetz W. 2014b. Data from: EltonTraits 1.0: Species-level foraging attributes of the world’s birds and mammals. https://esapubs.org/archive/ecol/E095/178/.
COI sequence data for this project were obtained from the Barcode of Life Data System (BOLD):
Ratnasingham, S., & Hebert, P. D. N. (2007). bold: The Barcode of Life Data System (http://www.barcodinglife.org). Molecular Ecology Notes, 7(3), 355–364. https://doi.org/10.1111/j.1471-8286.2007.01678.x.
Nuclear sequence data for this project were obtained from:
Burleigh JG, Kimball RT, Braun EL. 2015b. Data from: Building the avian tree of life using a large-scale, sparse supermatrix. Dryad Dataset. https://doi.org/10.5061/dryad.r6b87.
Pyron, R. A., Burbrink, F. T., & Wiens, J. J. (2013). Data from: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. Dryad Dataset. https://doi.org/10.5061/dryad.82h0m
Rabosky DL, Chang J, Title PO, Cowman PF, Sallan L, Friedman M, Kaschner K, Garilao C, Near TJ, Coll M, et al. 2019. Data from: An inverse latitudinal gradient in speciation rate for marine fishes. https://doi.org/10.5061/dryad.fc71cp4.
Upham NS, Essenstyn JA, Jetz W. 2019b. Data from: Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. Dryad Dataset. https://doi.org/10.5061/dryad.tb03d03.