Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish

Understanding whether small populations with low genetic diversity can
respond to rapid environmental change via phenotypic plasticity is an
outstanding research question in biology. RNA sequencing (RNA-seq) has
recently provided the opportunity to examine variation in gene expression,
a surrogate for phenotypic variation, in non-model species. We used a
comparative RNA-seq approach to assess expression variation within and
among adaptively divergent populations of a threatened freshwater fish,
Nannoperca australis, found across a steep hydroclimatic gradient in the
Murray-Darling Basin, Australia. These populations evolved under
contrasting selective environments (e.g. dry/hot lowland; wet/cold upland)
and represent opposite ends of the species’ spectrum of genetic diversity
and population size. We tested the hypothesis that environmental variation
among isolated populations has driven the evolution of divergent
expression at ecologically important genes using differential expression
(DE) analysis and an ANOVA-based comparative phylogenetic expression
variance and evolution model framework based on 27,425 de novo assembled
transcripts. Additionally, we tested whether gene expression variance
within-populations was correlated with levels of standing genetic
diversity. We identified 290 DE candidate transcripts, 33 transcripts with
evidence for high expression plasticity, and 50 candidates for divergent
selection on gene expression after accounting for phylogenetic structure.
Variance in gene expression appeared unrelated to levels of genetic
diversity. Functional annotation of the candidate transcripts revealed
variation in water quality is an important factor influencing expression
variation for N. australis. Our findings suggest that gene expression
variation can contribute to the evolutionary potential of small
populations.