Evolutionary history of the Hymenoptera - Supplementary Datasets

Published: 22 Mar 2017 | Version 3 | DOI: 10.17632/trbj94zm2n.3
Contributor(s):
  • Ralph Peters,
    Ralph Peters
    Center of Taxonomy and Evolutionary Research, Arthropoda Department, Zoologisches Forschungmuseum Alexander Koenig, Bonn, Germany
    First and corresponding author
  • Lars Krogmann,
    Agricultural and Biological Sciences
    Entomologie, Staatliches Museum für Naturkunde Stuttgart, 70191 Stuttgart, Germany
  • Christoph Mayer,
    Nursing and Health Professions
    Center for Molecular Biodiversity Research,Zoologisches Forschungsmuseum Koenig, Bonn, Germany
  • Alexander Donath,
    Alexander Donath
    Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
  • Simon Gunkel,
    Earth and Planetary Sciences
    Steinmann Institut für Geologie, Mineralogie und Paläontologie, 53115 Bonn, Germany
  • Karen Meusemann,
    Karen Meusemann
    Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, 79104 Freiburg (Brsg.), Germany
  • Alexey Kozlov,
    Computer Science
    Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
  • Lars Podsiadlowski,
    Agricultural and Biological Sciences
    Institute of Evolutionary Biology and Ecology, University of Bonn, 53121 Bonn, Germany
  • Malte Petersen,
    Malte Petersen
    Center for Molecular Biodiversity Research, Zoologisches Forschungmuseum Alexander Koenig, Bonn, Germany
  • Rob Lanfear,
    Rob Lanfear
    Ecology, Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
  • Patricia Dietz,
    Patricia Dietz
    Centro de Investigaciones y Transferencia de Catamarca, CITCA-CONICET/UNCA, Catamarca, Argentina
  • John Heraty,
    John Heraty
    Department of Entomology, University of California, Riverside, CA, 92521, USA
  • Karl Kjer,
    Agricultural and Biological Sciences
    Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
  • Seraina Klopfstein,
    Seraina Klopfstein
    Naturhistorisches Museum der Burgergemeinde Bern, 3005 Bern, Switzerland
  • Rudolf Meier,
    Rudolf Meier
    Department of Biological Sciences and Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117543, Singapore
  • Carlo Polidori,
    Carlo Polidori
    Instituto de Ciencias Ambientales (ICAM), Universidad de Castilla-La Mancha, 45071 Toledo, Spain
  • Thomas Schmitt,
    Thomas Schmitt
    Department of Animal Ecology and Tropical Biology, University of Würzburg, 97074 Würzburg, Germany
  • Shanlin Liu,
    Shanlin Liu
    China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, China 518083, People’s Republic of China
  • Xin Zhou,
    Xin Zhou
    Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People’s Republic of China
  • Torsten Wappler,
    Torsten Wappler
    Steinmann Institut für Geologie, Mineralogie und Paläontologie, 53115 Bonn, Germany
  • Jes Rust,
    Jes Rust
    Steinmann Institut für Geologie, Mineralogie und Paläontologie, 53115 Bonn, Germany
  • Bernhard Misof,
    Bernhard Misof
    Center for Molecular Biodiversity Research, Zoologisches Forschungmuseum Alexander Koenig, Bonn, Germany
  • Oliver Niehuis
    Oliver Niehuis
    Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, 79104 Freiburg (Brsg.), Germany
    Senior and corresponding author

Description of this data

Data deposited for the paper:
Evolutionary history of the Hymenoptera

  1. Folder name:
    1-Gene-MSAs_after-pal2nal

    Kind of data:
    Multiple sequence alignments of orthologous genes after alignment refinement (aa and nt data).

  2. Folder name:
    2-Main-dataset_dataBlocks-PartitionfinderResults-Final-supermatrix

    Kind of data and file formats:
    • Main data set: Concatenated supermatrices after the Aliscore and Mare step. Sites have been rearranged according to clan, Pfam-A, Pfam-B and void data blocks. Files are in phylip format.
    • Corresponding data block files are given as text files. Data blocks and the supermatices are used as input for the PartitionFinder analysis.
    • Results of the PartitionFinder analysis: Best partitioning scheme in RAxML partition file format.
    • Files that contain the word “reduced” in their name are the alignment and partition file produced by RAxML when automatically filtering alignment sites, which contain only gap and ambiguous characters.
    • All above files are given for aa and nt data sets.

  1. Folder name:
    3-datasets_decisive-datasets

    Kind of data and file formats:
    As in number 2) but for the data sets reduced to the decisive data sets. That is, data blocks with missing data in required taxonomic groups has been removed. Decisive data sets are: Aculeata-decisive-dataset, Apoidea-decisive-dataset, Backbone-decisive-dataset.

  2. Folder name:
    4-datasets_FCLM_and_permutations

    Kind of data and file formats:
    Data sets used for the Four Cluster Likelihood Mapping method. Files include the partition files in RAxML Format, the taxonomic group files as well as the necessary data sets from which the permutations have been generated. For detail on the methods and the purpose of the permutation test see the Supplemental Experimental Procedures (available online). The generating scripts for the permuted data sets are available upon request. Permuted data sets can also be created by following the description in the Supplemental Experimental Procedures. The reduced matrix is the matrix that was used as input in the permutation script.

  3. Folder name:
    5-results_rogue_taxa_analyses

    Kind of data and file formats:
    Result files of the program RogueNaRok for different parameters. Results are given for the analyses conducted for the aa and the nt data sets.

  4. Folder name:
    6-results_tree_reconstruction_decisive_datasets

    Kind of data and file formats:
    Resulting phylogenetic trees in Newick format for the decisive data sets.

  5. Folder name:
    7-results_FCLM_and_permutations

    Kind of data and file formats:
    Result files of the FCLM analysis. Files are graphic files in the SVG format.

  6. Folder name:
    8-results_tree-reconstruction_main_analysis

    Kind of data and file formats:
    Resulting phylogenetic trees in Newick format of the main analysis.

  7. Folder name:
    9-dating_dataset_and_results

    Kind of data and file formats:
    Input and result files of the dating analysis.

Experiment data files

This data is associated with the following publication:

Evolutionary History of the Hymenoptera

Published in: Current Biology

Latest version

  • Version 3

    2017-03-22

    Published: 2017-03-22

    DOI: 10.17632/trbj94zm2n.3

    Cite this dataset

    Peters, Ralph; Krogmann, Lars; Mayer, Christoph; Donath, Alexander; Gunkel, Simon; Meusemann, Karen; Kozlov, Alexey; Podsiadlowski, Lars; Petersen, Malte; Lanfear, Rob; Dietz, Patricia; Heraty, John; Kjer, Karl; Klopfstein, Seraina; Meier, Rudolf; Polidori, Carlo; Schmitt, Thomas; Liu, Shanlin ; Zhou, Xin; Wappler, Torsten; Rust, Jes; Misof, Bernhard; Niehuis, Oliver (2017), “Evolutionary history of the Hymenoptera - Supplementary Datasets”, Mendeley Data, v3 http://dx.doi.org/10.17632/trbj94zm2n.3

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