DOI: 10.5061/dryad.v0s27
title: Data from: Automated integration of trees and traits: a case study using paired fin loss across teleost fishes

description: Data synthesis required for large-scale macroevolutionary studies is
 challenging with the current tools available for integration. Using a
 classic question regarding the frequency of paired fin loss in teleost
 fishes as a case study, we sought to create automated methods to
 facilitate the integration of broad-scale trait data with a sizable
 species-level phylogeny. Similar to the evolutionary pattern previously
 described for limbs, pelvic and pectoral fin reduction and loss are
 thought to have occurred independently multiple times in the evolution of
 fishes. We developed a bioinformatics pipeline to identify the presence
 and absence of pectoral and pelvic fins of 12,582 species. To do this, we
 integrated a synthetic morphological supermatrix of phenotypic data for
 the pectoral and pelvic fins for teleost fishes from the Phenoscape
 Knowledgebase (two presence/absence characters for 3,047 taxa) with a
 species-level tree for teleost fishes from the Open Tree of Life project
 (38,419 species). The integration method detailed herein harnessed a new
 combined approach by utilizing data based on ontological inference, as
 well as phylogenetic propagation, to reduce overall data loss. Using
 inference enabled by ontology-based annotations, missing data were reduced
 from 98.0% to 85.9%, and further reduced to 34.8% by phylogenetic data
 propagation. These methods allowed us to extend the data to an additional
 11,293 species for a total of 12,582 species with trait data. The pectoral
 fin appears to have been independently lost in a minimum of 19 lineages
 and the pelvic fin in 48. Though interpretation is limited by lack of
 phylogenetic resolution at the species level, it appears that following
 loss, both pectoral and pelvic fins were regained several (3) to many (14)
 times respectively. Focused investigation into putative regains of the
 pectoral fin, all within one clade (Anguilliformes), showed that the
 pectoral fin was regained at least twice following loss. Overall, this
 study points to specific teleost clades where strategic phylogenetic
 resolution and genetic investigation will be necessary to understand the
 pattern and frequency of pectoral fin reversals.
description: 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).