Convergent patterns of gene expression and protein evolution associated with adaptation to desert environments in rodents

Desert specialization has arisen multiple times across rodents and is often associated with a suite of convergent phenotypes, including modification of the kidneys to mitigate water loss. However, the extent to which phenotypic convergence in desert rodents is mirrored on the molecular level is unknown. Here, we sequenced kidney mRNA and assembled transcriptomes of three pairs of rodent species to search for convergence in gene expression and amino acid sequence associated with adaptation to deserts. We conducted phylogenetically-independent comparisons between a desert specialist and a non-desert relative in three families representing ~70 million years of evolution. Overall patterns of gene expression faithfully recapitulated the phylogeny of these six taxa. However, we found that 14% of all genes tested showed convergent patterns of expression evolution between desert and non-desert taxa, a proportion that is much higher than expected by chance. In addition to these convergent changes, we observed many species-pair specific changes in gene expression indicating that different instances of adaptation to deserts include a combination of unique and shared changes. Patterns of protein evolution revealed a small number of genes showing evidence of positive selection, and most of these did not show convergent changes in gene expression. Convergence in gene expression was more frequent than convergence in amino acid sequence, suggesting that changes in gene regulation play a primary role in desert adaptation in rodents.