DOI: 10.5061/dryad.n10j0
title: Data from: Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles

description: Scarab beetles exhibit an astonishing variety of rigid exo-skeletal
 outgrowths, known as “horns”. These traits are often sexually dimorphic
 and vary dramatically across species in size, shape, location, and
 allometry with body size. In many species, the horn exhibits
 disproportionate growth resulting in an exaggerated allometric
 relationship with body size, as compared to other traits, such as wings,
 that grow proportionately with body size. Depending on the species, the
 smallest males either do not produce a horn at all, or they produce a
 disproportionately small horn for their body size. While the diversity of
 horn shapes and their behavioural ecology have been reasonably well
 studied, we know far less about the proximate mechanisms that regulate
 horn growth. Thus, using 454 pyrosequencing, we generated transcriptome
 profiles, during horn growth and development, in two different scarab
 beetle species: the Asian rhinoceros beetle, Trypoxylus dichotomus, and
 the dung beetle, Onthophagus nigriventris. We obtained over half a million
 reads for each species that were assembled into over 6,000 and 16,000
 contigs respectively. We combined these data with previously published
 studies to look for signatures of molecular evolution. We found a small
 subset of genes with horn-biased expression showing evidence for recent
 positive selection, as is expected with sexual selection on horn size. We
 also found evidence of relaxed selection present in genes that
 demonstrated biased expression between horned and horn-less morphs,
 consistent with the theory of developmental decoupling of phenotypically
 plastic traits.
description: T. dichotomus: NCBI
 accession codesAccession codes for the
 T. dichotomus bioproject, assembly, and raw reads.tdicho_NCBI_codes.txtO. nigriventris NCBI accession codesNCBI accession codes for O. nigriventris, bioproject, assembly and raw reads.onig_NCBI_codes.txtGO terms retrievedA full list of GO terms retrieved from a BLASTx search against a Uniprot/SwissProt database. This is for both the T.dichotmous and O.nigriventris assemblies.GO_terms.xlsxSNPs for O. taurus and T. dichotomusA list of putative SNPs found in the assemblies for T. dichotomus and O. nigriventris. See main manuscript for more details.SNPs.xlsxT. dichotomus transcriptome assemblyNewbler gsAssembler v 2.8 (Roche, Switzerland; seed step = 12, seed length = 16, seed count = 1, minimum overlap length = 40, minimum overlap identity =90%, alignment identity score = 2, alignment difference score = -3). This assembly has not be filtered like the version available on the NCBI (NCBI filters: length &gt; 200bp, &lt;10% N's, &lt;14c consecutive N's)tdicho_assembly.fasta.zipO. nigriventris transcriptome assemblyNewbler gsAssembler v 2.8 (Roche, Switzerland; seed step = 12, seed length = 16, seed count = 1, minimum overlap length = 40, minimum overlap identity =90%, alignment identity score = 2, alignment difference score = -3). This assembly has not be filtered like the version available on the NCBI (NCBI filters: length &gt; 200bp, &lt;10% N's, &lt;14 consecutive N's)onig_assembly.fasta.zipO. taurus altered assemblyThe O. taurus 454 assembly from Choi et al 2011 was merged with an O. taurus EST assembly from Kijimoto et al 2009. See the manuscript for more details.otaurus_assembly.fasta.zipKa/Ks estimation pipelineThe custom python scripts required for Ka/Ks estimation.kaks_pipleline.zipKa/Ks and developmental decoupling analysis r-scriptr-script required for running statistical analysis of the Ka/Ks estimations and developmental decoupling.kaks_analysis.rO. taurus developmental decoupling valuesThe values used for the developmental decoupling analysis. This is a merged version of what was published in Snell-Rood et al 2011 (Evolution 65: 231–245). See Warren et al 2014 for more details on how they were merged.devdecoupling.xlsO. taurus vs O. nigriventris developmental decoupling analysis inputInput file for developmental decoupling statistical analysis for O. taurus vs O. nigriventrisot_on_kaks_input.csvO. taurus vs T. dichotomus developmental decoupling analysis inputInput file for developmental decoupling statistical analysis for O. taurus vs T. dichotomus.ot_td_kaks_input.csv