Captivity induces large and population-dependent brain transcriptomic changes in wild-caught cane toads (Rhinella marina)

Abstract

Gene expression levels are key molecular phenotypes at the interplay between genotype and environment. Mounting evidence suggests that short-term changes in environmental conditions, such as those encountered in captivity, can substantially affect gene expression levels. Yet, the exact magnitude of this effect, how general it is, and whether it results in parallel changes across populations are not well understood. Here, we take advantage of the well-studied cane toad, Rhinella marina, to examine the effect of short-term captivity on brain gene expression levels, and determine whether effects of captivity differ between long-colonized and vanguard populations of the cane toad's Australian invasion range. We compared the transcriptomes of wild-caught toads immediately assayed with those from toads captured from the same populations but maintained in captivity for seven months. We found large differences in gene expression levels between captive and wild-caught toads from the same population, with an over-representation of processes related to behaviour and the response to stress. Captivity had a much larger effect on both gene expression levels and gene expression variability in toads from vanguard populations compared to toads from long-colonized areas, potentially indicating an increased plasticity in toads at the leading edge of the invasion. Overall, our findings indicate that short-term captivity can induce large and population-specific transcriptomic changes, which has significant implications for studies comparing phenotypic traits of wild-caught organisms from different populations that have been held in captivity.

Keywords: Bufo marinus; cane toad; captivity; invasive species; population; transcriptomics.

FIGURE 1

Location of samples. NT, Northern Territory; QLD, Queensland; SWA, Western Australia. The shaded area represents the cane toad's Australian invasion range

FIGURE 2

Brain gene expression differences between captive and wild‐caught cane toads from range‐core populations. (a) Heatmap of normalized gene expression values for all differentially expressed genes (DEGs) between captive and wild‐caught toads. Columns correspond to individuals. Rows correspond to genes. Colour depicts Z‐score normalized gene expression value. (b) Volcano plot of significantly DEGs between captive and wild‐caught toads. Nonsignificant genes are represented in grey. (c) GO enrichment analysis of all DEGs between captive and wild‐caught toads. The size of each circle is proportional to the number of genes being significantly enriched, while the colour of each circle is proportional to its FDR‐corrected p‐value. Gene ratio corresponds to the proportion of genes being enriched out of the total number of genes in that GO category. BP, biological process; CC, cellular component; MF, molecular function

FIGURE 3

Brain gene expression differences between captive and wild‐caught cane toads from range‐front populations. (a) Heatmap of normalized gene expression values for all differentially expressed genes (DEGs) between captive and wild‐caught toads. Columns correspond to individuals. Rows correspond to genes. Colour depicts Z‐score normalized gene expression value. (b) Volcano plot of significantly DEGs between captive and wild‐caught toads. Nonsignificant genes are represented in grey. (c) Gene ontology (GO) enrichment analysis of all DEGs between captive and wild‐caught toads. The size of each circle is proportional to the number of genes being significantly enriched, while the colour of each circle is proportional to its false discovery rate (FDR)‐corrected p‐value. Gene ratio corresponds to the proportion of genes being enriched out of the total number of genes in that GO category. BP, biological process; CC, cellular component; MF, molecular function

FIGURE 4

Comparison of the brain transcriptomic differences in captive versus wild‐caught cane toads between range‐core and range‐front populations. (a) Venn diagram representing the overlap of differentially expressed genes (DEGs) in captive versus wild‐caught toads between range‐core and range‐front populations. (b) Upset plot representing the overlap of DEGs showing up‐ or downregulation in captive versus wild‐caught toads between range‐core and range‐front populations. Vertical barplots show the number of genes in any particular combination represented by dots with connecting lines. Genes in this plot correspond to the 504 DEGs overlapping between range‐core and range‐front populations. (c–e) Gene ontology (GO)enrichment analysis of DEGs between captive and wild‐caught toads (c) unique to range‐core populations, (d) shared between range‐core and range‐front populations, (e) unique to range‐front populations. The size of each circle is proportional to the number of genes being significantly enriched, while the colour of each circle is proportional to its FDR‐corrected p‐value. Gene ratio corresponds to the proportion of genes being enriched out of the total number of genes in that GO category. BP, biological process; CC, cellular component; MF, molecular function

FIGURE 5

Brain gene expression variability between captive and wild‐caught cane toads from range‐core and range‐front populations. (a, b) Volcano plots of significantly differentially dispersed genes between captive and wild‐caught toads from (a) range‐core populations, and (b) range‐front populations. Nonsignificant genes are represented in grey