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.
T. dichotomus: NCBI accession codes
Accession codes for the T. dichotomus bioproject, assembly, and raw reads.
O. nigriventris NCBI accession codes
NCBI accession codes for O. nigriventris, bioproject, assembly and raw reads.
GO terms retrieved
A 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.
SNPs for O. taurus and T. dichotomus
A list of putative SNPs found in the assemblies for T. dichotomus and O. nigriventris. See main manuscript for more details.
T. dichotomus transcriptome assembly
Newbler 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 > 200bp, <10% N's, <14c consecutive N's)
O. nigriventris transcriptome assembly
Newbler 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 > 200bp, <10% N's, <14 consecutive N's)
O. taurus altered assembly
The 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.
Ka/Ks estimation pipeline
The custom python scripts required for Ka/Ks estimation.
Ka/Ks and developmental decoupling analysis r-script
r-script required for running statistical analysis of the Ka/Ks estimations and developmental decoupling.
O. taurus developmental decoupling values
The 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.
O. taurus vs O. nigriventris developmental decoupling analysis input
Input file for developmental decoupling statistical analysis for O. taurus vs O. nigriventris
O. taurus vs T. dichotomus developmental decoupling analysis input
Input file for developmental decoupling statistical analysis for O. taurus vs T. dichotomus.