The process of biological invasion exposes a species to novel pressures, in terms of both the environments it encounters and the evolutionary consequences of range expansion. Several invaders have been shown to exhibit rapid evolutionary changes in response to those pressures, thus providing robust opportunities to clarify the processes at work during rapid phenotypic transitions. The accelerating pace of invasion of cane toads (Rhinella marina) in tropical Australia during its 80-year history has been well characterized at the phenotypic level, including common-garden experiments that demonstrate heritability of several dispersal-relevant traits. Individuals from the invasion front (and their progeny) show distinctive changes in morphology, physiology and behaviour that, in combination, result in far more rapid dispersal than is true of conspecifics from long-colonized areas. The extensive body of work on cane toad ecology enables us to place into context studies of the genetic basis of these traits. Our analyses of differential gene expression from toads from both ends of this invasion-history transect reveal substantial upregulation of many genes, notably those involved in metabolism and cellular repair. Clearly, then, the dramatically rapid phenotypic evolution of cane toads in Australia has been accompanied by substantial shifts in gene expression, suggesting that this system is well suited to investigating the genetic underpinnings of invasiveness.
CaneToad_muscle_denovo_transcriptome_Australia
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
CaneToad_muscle_transcriptome_Australia.fasta
CaneToad_West_vs_East_Differential_expression_results
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.
CaneToad_West_vs_East_noercc.edgeR.DE_results
RSEM_expression_counts
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).