Data from: Flight loss linked to faster molecular evolution in insects

 

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Title 1. Whole-tree dN/dS and overall substitution rates analysis
Description This folder contains the input and output files used in and obtained from the program PAML (Yang 2007) for the whole-tree analysis of dN/dS ratios (program component codeml) and overall substitution rates (program component baseml). This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Note both analyses types (codeml and baseml) use the same tree and nucleotide files. Each gene folder contains 6 files: 2 control files (1 codeml, 1 baseml - “.ctl”), 1 nucleotide file (“.nuc”), 1 tree file (“.trees”), 2 output files (1 codeml, 1 baseml).
Download 1. Whole-tree dNdS and Rates.zip (713.0 Kb)
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Title 2. dN/dS ratio sister-clades analysis
Description This folder contains the input and output files used in and obtained from the program PAML (Yang 2007) for the sister-clade analysis of dN/dS ratios (program component codeml). This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Each gene folder contains 4 files: 1 control file (“.ctl”), 1 nucleotide file (“.nuc”), 1 tree file (“.trees”), and 1 output file.
Download 2. dNdS sister clades.zip (600.1 Kb)
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Title 3. Relative rates sister-clades analysis
Description This folder contains the input and output files used in and obtained from the program Phyltest (Phyltest v.2.0, http://www.kumarlab.net/publications) for the sister-clade relative rates analysis. This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Transitions are identified by the set# in the file name (e.g. “Set1” or “S1” = transition #1, transitions as described in the Supplementary Material). All transitions were analysed with separate input and output files except for the transitions within the source study folder Cunha et al. 2011 where each transition was run from the same file per gene. Within the input files the abbreviations FL=flightless, F=flight-capable, OG=outgroup, and the number after these identifiers signifies the transition. Each gene folder (except where just described) contains 2 files per transition: 1 input file (nucleotide - “.dat”) and 1 output file.
Download 3. Relative rates sister clades.zip (137.5 Kb)
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When using this data, please cite the original publication:

Mitterboeck TF, Adamowicz SJ (2013) Flight loss linked to faster molecular evolution in insects. Proceedings of the Royal Society B 280(1767): 20131128. http://dx.doi.org/10.1098/rspb.2013.1128

Additionally, please cite the Dryad data package:

Mitterboeck TF, Adamowicz SJ (2013) Data from: Flight loss linked to faster molecular evolution in insects. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3ps4r
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