DOI: 10.5061/dryad.m5298
title: Data from: A genetic perspective on rapid evolution in cane toads (Rhinella marina)

description: 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.
description: CaneToad_muscle_denovo_transcriptome_AustraliaDe 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 formatCaneToad_muscle_transcriptome_Australia.fastaCaneToad_West_vs_East_Differential_expression_resultsDifferential 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_resultsRSEM_expression_countsIndividual 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).