Data from: Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles

Warren IA, Vera JC, Johns A, Zinna R, Marden JH, Emlen DJ, Dworkin I, Lavine LC

Date Published: February 24, 2014

DOI: http://dx.doi.org/10.5061/dryad.n10j0

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title T. dichotomus: NCBI accession codes
Downloaded 13 times
Description Accession codes for the T. dichotomus bioproject, assembly, and raw reads.
Download tdicho_NCBI_codes.txt (968 bytes)
Details View File Details
Title O. nigriventris NCBI accession codes
Downloaded 10 times
Description NCBI accession codes for O. nigriventris, bioproject, assembly and raw reads.
Download onig_NCBI_codes.txt (263 bytes)
Details View File Details
Title GO terms retrieved
Downloaded 39 times
Description 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.
Download GO_terms.xlsx (820.2 Kb)
Details View File Details
Title SNPs for O. taurus and T. dichotomus
Downloaded 39 times
Description A list of putative SNPs found in the assemblies for T. dichotomus and O. nigriventris. See main manuscript for more details.
Download SNPs.xlsx (1.405 Mb)
Details View File Details
Title T. dichotomus transcriptome assembly
Downloaded 47 times
Description 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)
Download tdicho_assembly.fasta.zip (4.658 Mb)
Details View File Details
Title O. nigriventris transcriptome assembly
Downloaded 34 times
Description 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)
Download onig_assembly.fasta.zip (11.33 Mb)
Details View File Details
Title O. taurus altered assembly
Downloaded 36 times
Description 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.
Download otaurus_assembly.fasta.zip (8.877 Mb)
Details View File Details
Title Ka/Ks estimation pipeline
Downloaded 42 times
Description The custom python scripts required for Ka/Ks estimation.
Download kaks_pipleline.zip (63.44 Kb)
Details View File Details
Title Ka/Ks and developmental decoupling analysis r-script
Downloaded 22 times
Description r-script required for running statistical analysis of the Ka/Ks estimations and developmental decoupling.
Download kaks_analysis.r (23.60 Kb)
Details View File Details
Title O. taurus developmental decoupling values
Downloaded 69 times
Description 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.
Download devdecoupling.xls (1.851 Mb)
Details View File Details
Title O. taurus vs O. nigriventris developmental decoupling analysis input
Downloaded 12 times
Description Input file for developmental decoupling statistical analysis for O. taurus vs O. nigriventris
Download ot_on_kaks_input.csv (63.68 Kb)
Details View File Details
Title O. taurus vs T. dichotomus developmental decoupling analysis input
Downloaded 8 times
Description Input file for developmental decoupling statistical analysis for O. taurus vs T. dichotomus.
Download ot_td_kaks_input.csv (35.69 Kb)
Details View File Details

When using this data, please cite the original publication:

Warren IA, Vera JC, Johns A, Zinna R, Marden JH, Emlen DJ, Dworkin I, Lavine LC (2014) Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles. PLoS ONE 9(2): e88364. http://dx.doi.org/10.1371/journal.pone.0088364

Additionally, please cite the Dryad data package:

Warren IA, Vera JC, Johns A, Zinna R, Marden JH, Emlen DJ, Dworkin I, Lavine LC (2014) Data from: Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n10j0
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: