Data from: Automated integration of trees and traits: a case study using paired fin loss across teleost fishes

README fileSupplementary Materials File 1Teleostei species-level tree from Open Tree. Tree description file (Newick) from Open Tree synthesis used as the input into Mesquite.Supplementary Materials File 2Output files of synthesis tree build from Open Tree. Archive files of the output directory for each step in the synthesis tree build.Supplementary Materials File 3Merged tree matrix. NEXUS-formatted translation of the final output matrix (Supplementary Materials Matrix 4) merged with the Teleostei species-level tree from Open Tree (Supplementary Materials File 1). This combined matrix and tree file was used for ancestral state reconstruction in Mesquite.Supplementary Materials File 4Anguilliformes species-level trees based on subset from Teleostei species-level tree from Open Tree (Supplementary Materials File 1) merged with the final output matrix (Supplementary Materials Matrix 4). File includes 1,000 trees each with randomly resolved polytomies performed using the APE package in R.Supplementary Materials Matrix 1OntoTrace generated NeXML synthetic morphological supermatrix for pectoral fin and pelvic fin presence and absence, including metadata for supporting states and publication information.Supplementary Materials Matrix 2The tab-delimited character matrix generated after pre-processing the OntoTrace matrix (Supplementary Materials Matrix 1) by converting from NeXML format.Supplementary Materials Matrix 3Resulting matrix after the propagation step. The taxon names are based on the VTO, and this matrix is the input for the taxon name reconciliation step.Supplementary Materials Matrix 4Final output matrix of the pipeline. This tab-delimited file was read into Mesquite v3.10 for mapping onto the Teleostei species-level tree (Supplementary Materials File 1).Supplementary Materials Table 1List of 87 publications used in constructing the synthetic supermatrix, including the number of taxa, pectoral and pelvic fin characters, and states. Studies that were specifically curated for the purpose of more fully representing the distribution of pelvic and pectoral fin conditions across teleosts are denoted by an asterisk.Supplementary Materials Table 2Comparison of valid teleost species between FishBase (CoF), and Open Tree.Supplementary Materials Table 3Comparison of teleost families between the Vertebrate Taxonomy Ontology (VTO), Open Tree, and Catalog of Fishes (CoF). Dash indicates family name that is not recognized within a particular source.Supplementary Materials Table 4Statistics for reconciliation between Vertebrate Taxonomy Ontology (VTO) and Open Tree taxa. This file lists the species with data that were mismatched during the reconciliation step, and they are separated based on the reason for the mismatch (due to species being extinct, unconventional naming, etc.).Supplementary Materials Table 5List of VTO teleost families that show pectoral fin absence, pelvic fin absence, or the absence of both paired fins. Families with pelvic fin absence were compared to previously documented families (Nelson 1990), and details given in footnotes.Supplementary Materials Table 6Ancestral state reconstruction across Anguilliformes Open Tree phylogeny (Supplementary Materials File 4) for pectoral fin gain and loss (Fig. 7).