DOI: 10.5061/dryad.3ps4r
title: Data from: Flight loss linked to faster molecular evolution in insects

description: The loss of flight ability has occurred thousands of times independently
 during insect evolution. Flight loss may be linked to higher molecular
 evolutionary rates because of reductions in effective population sizes
 (Ne) and relaxed selective constraints. Reduced dispersal ability
 increases population subdivision, may decrease geographical range size and
 increases (sub)population extinction risk, thus leading to an expected
 reduction in Ne. Additionally, flight loss in birds has been linked to
 higher molecular rates of energy-related genes, probably owing to relaxed
 selective constraints on energy metabolism. We tested for an association
 between insect flight loss and molecular rates through comparative
 analysis in 49 phylogenetically independent transitions spanning multiple
 taxa, including moths, flies, beetles, mayflies, stick insects,
 stoneflies, scorpionflies and caddisflies, using available nuclear and
 mitochondrial protein-coding DNA sequences. We estimated the rate of
 molecular evolution of flightless (FL) and related flight-capable lineages
 by ratios of non-synonymous-to-synonymous substitutions (dN/dS) and
 overall substitution rates (OSRs). Across multiple instances of flight
 loss, we show a significant pattern of higher dN/dS ratios and OSRs in FL
 lineages in mitochondrial but not nuclear genes. These patterns may be
 explained by relaxed selective constraints in FL ectotherms relating to
 energy metabolism, possibly in combination with reduced Ne.
description: 1. Whole-tree dN/dS and
 overall substitution rates analysisThis 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).1. Whole-tree dNdS and
 Rates.zip2. dN/dS ratio
 sister-clades analysisThis 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.2. dNdS sister
 clades.zip3. Relative rates
 sister-clades analysisThis 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.3. Relative rates sister
 clades.zip