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 at the molecular level is unknown. Here, we sequenced kidney mRNA and assembled transcriptomes for 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 8.6% of all genes 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, the majority of which did not show convergent changes in gene expression. Overall, our results suggest convergent changes in gene regulation play a primary role in the complex trait of desert adaptation in rodents.

Compromised Function of the Pancreatic Transcription Factor PDX1 in a Lineage of Desert Rodents

Gerbils are a subfamily of rodents living in arid regions of Asia and Africa. Recent studies have shown that several gerbil species have unusual amino acid changes in the PDX1 protein, a homeodomain transcription factor essential for pancreatic development and β-cell function. These changes were linked to strong GC-bias in the genome that may be caused by GC-biased gene conversion, and it has been hypothesized that this caused accumulation of deleterious changes. Here we use two approaches to examine if the unusual changes are adaptive or deleterious. First, we compare PDX1 protein sequences between 38 rodents to test for association with habitat. We show the PDX1 homeodomain is almost totally conserved in rodents, apart from gerbils, regardless of habitat. Second, we use ectopic gene overexpression and gene editing in cell culture to compare functional properties of PDX1 proteins. We show that the divergent gerbil PDX1 protein inefficiently binds an insulin gene promoter and ineffectively regulates insulin expression in response to high glucose in rat cells. The protein has, however, retained the ability to regulate some other β-cell genes. We suggest that during the evolution of gerbils, the selection-blind process of biased gene conversion pushed fixation of mutations adversely affecting function of a normally conserved homeodomain protein. We argue these changes were not entirely adaptive and may be associated with metabolic disorders in gerbil species on high carbohydrate diets. This unusual pattern of molecular evolution could have had a constraining effect on habitat and diet choice in the gerbil lineage.

Physiological validation of a non-invasive method to evaluate adrenocortical activity and the time course for the excretion of stress hormones in the feces of three species of desert gerbils

We evaluated the suitability of a corticosterone enzyme immunoassay (EIA) to monitor excretion of fecal glucocorticoid metabolites (FGM) in response to Adrenocorticotropic hormone (ACTH) and saline injections in three desert rodent species (Gerbillus andersoni allenbyi (GA), Gerbillus nanus (GN), and Gerbilis piridium (GP). We exposed 24 gerbils (N = 9 for GA, N = 7 for GN, N = 8 for GP) to an ACTH and a saline injection at different times. Fecal samples were collected hourly for 24 hours after injection. The average starting concentration (baseline) FGM concentration was 797 ng/g for GA, 183 ng/g for GN, and 749 ng/g for GP. The average peak concentration was 2377 ng/g for GA, 589 ng/g for GN, and 1987 ng/g for GP. We were able to provide a physiological validation for the chosen assay in GAs and GPs, however, our results for GNs were less clear. We found an increase in FGM concentrations on average after 5.5 hours in GA, 3.1 hours in GN, and 3.8 hours in GP. We found a peak in FGM concentration on average after 8.8 hours in GA, 5.6 hours in GN, and 10.3 hours in GP. We determined that FGM concentration returned to starting value on average after 14.4 hours in GA, 9.1 hours in GN, and 15.1 hours in GP. The outcomes of this study can help establish trapping protocols and time frames for FGM monitoring of these wild small mammal populations. The time course for excretion of FGM is similar between the species in this study, and comparable to some non-desert rodents. We found high variation in the time course of excretion within species. This variation needs to be taken into account when monitoring stress responses in the field. By assessing adrenocortical activity using FGM monitoring, stress responses to varying ecological and environmental factors can be reliably examined in the field.

Day and night in the subterranean: measuring daily activity patterns of subterranean rodents (Ctenomys aff. knighti) using bio-logging

While most studies of the impacts of climate change have investigated shifts in the spatial distribution of organisms, temporal shifts in the time of activity is another important adjustment made by animals in a changing world. Due to the importance of light and temperature cycles in shaping activity patterns, studies of activity patterns of organisms that inhabit extreme environments with respect to the 24-hour cyclicity of Earth have the potential to provide important insights into the interrelationships among abiotic variables, behaviour and physiology. Our previous laboratory studies with Argentinean tuco-tucos from the Monte desert (Ctenomys aff. knighti) show that these subterranean rodents display circadian activity/rest rhythms that can be synchronized by artificial light/dark cycles. Direct observations indicate that tuco-tucos emerge mainly for foraging and for removal of soil from their burrows. Here we used bio-logging devices for individual, long-term recording of daily activity/rest (accelerometry) and time on surface (light-loggers) of six tuco-tucos maintained in outdoor semi-natural enclosures. Environmental variables were measured simultaneously. Activity bouts were detected both during day and night but 77% of the highest values happened during the daytime and 47% of them coincided with time on surface. Statistical analyses indicate time of day and temperature as the main environmental factors modulating time on surface. In this context, the total duration that these subterranean animals spent on surface was high during the winter, averaging 3 h per day and time on surface occurred when underground temperature was lowest. Finally, transport of these animals to the indoor laboratory and subsequent assessment of their activity rhythms under constant darkness revealed a switch in the timing of activity. Plasticity of activity timing is not uncommon among desert rodents and may be adaptive in changing environments, such as the desert where this species lives.