Data from: A genetic perspective on rapid evolution in cane toads (Rhinella marina)

Rollins LA, Richardson MF, Shine R

Date Published: March 31, 2015



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Title CaneToad_muscle_denovo_transcriptome_Australia
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Description De novo transcriptome assembly of Cane toad muscle (triceps femurs) tissue using the Trinity assembler, with default settings. We filtered out any transcripts with less that 1% of the per-gene expression level using a script bundled with Trinity. Raw reads from one individual per geographic population (RM0021M, RM0094M, RM0108M and RM0169M) were pooled to produce the representative read set across all populations that was used in de novo assembly. File contains assembled sequences in fast format
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Title CaneToad_West_vs_East_Differential_expression_results
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Description Differential gene expression results in invasive Cane toad muscle tissue between the Western Australia range edge (West) and the Queensland range core (East). Results produced in edgeR from associated RSEM individual expression count files (See attached archive). In edgeR testing was conducted using the classic approach for two groups, CPM-filtered counts were TMM-normalised, quantile-adjusted conditional maximum likelihood method was used to estimate dispersions and the exact test was used to call differentially expressed genes and compute p-values. Columns are: transcript ID, Log Fold-change between the regions (-ve values donate down-regulation in the West and +ve the opposite), Log CPM (counts per million mapped reads), P-value of differential expression, FDR is False discovery rate.
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Title RSEM_expression_counts
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Description Individual sample RSEM (v1.2.14 ) expression counts used for differential expression analysis. Each file in the archive corresponds to a separate individual (Individual membership to each population is given in TableS1 and the associated ReadMe file here). Columns are: transcript ID as in the fasta file, gene ID, transcript length, effective length, expected count, TPM (Transcripts Per Million), FPKM (Fragments Per Kilobase of transcript per Million mapped reads), IsoPct (Isoform percentage, it is the percentage of this transcript's abandunce over its parent gene's abandunce).
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When using this data, please cite the original publication:

Rollins LA, Richardson MF, Shine R (2015) A genetic perspective on rapid evolution in cane toads (Rhinella marina). Molecular Ecology 24(9): 2264-2276.

Additionally, please cite the Dryad data package:

Rollins LA, Richardson MF, Shine R (2015) Data from: A genetic perspective on rapid evolution in cane toads (Rhinella marina). Dryad Digital Repository.
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