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

Jackson LM, Fernando PC, Hanscom JS, Balhoff JP, Mabee PM

Date Published: January 5, 2018

DOI: https://doi.org/10.5061/dryad.v0s27.2

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Title README file
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Title Supplementary Materials File 1
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Description Teleostei species-level tree from Open Tree. Tree description file (Newick) from Open Tree synthesis used as the input into Mesquite.
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Title Supplementary Materials File 2
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Description Output files of synthesis tree build from Open Tree. Archive files of the output directory for each step in the synthesis tree build.
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Title Supplementary Materials File 3
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Description Merged 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.
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Title Supplementary Materials File 4
Description Anguilliformes 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.
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Title Supplementary Materials Matrix 1
Description OntoTrace generated NeXML synthetic morphological supermatrix for pectoral fin and pelvic fin presence and absence, including metadata for supporting states and publication information.
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Title Supplementary Materials Matrix 2
Description The tab-delimited character matrix generated after pre-processing the OntoTrace matrix (Supplementary Materials Matrix 1) by converting from NeXML format.
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Title Supplementary Materials Matrix 3
Description Resulting 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.
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Title Supplementary Materials Matrix 4
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Description Final 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).
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Title Supplementary Materials Table 1
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Description List 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.
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Title Supplementary Materials Table 2
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Description Comparison of valid teleost species between FishBase (CoF), and Open Tree.
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Title Supplementary Materials Table 3
Description Comparison 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.
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Title Supplementary Materials Table 4
Description Statistics 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.).
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Title Supplementary Materials Table 5
Description List 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.
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Title Supplementary Materials Table 6
Description Ancestral state reconstruction across Anguilliformes Open Tree phylogeny (Supplementary Materials File 4) for pectoral fin gain and loss (Fig. 7).
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When using this data, please cite the original publication:

Jackson LM, Fernando PC, Hanscom JS, Balhoff JP, Mabee PM (2018) Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syx098

Additionally, please cite the Dryad data package:

Jackson LM, Fernando PC, Hanscom JS, Balhoff JP, Mabee PM (2018) Data from: Automated integration of trees and traits: a case study using paired fin loss across teleost fishes. Dryad Digital Repository. https://doi.org/10.5061/dryad.v0s27.2
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