Kangaroo rats (Dipodomys sp.) and other members of the Heteromyidae have long been noted for their ability to limit water loss through the production of highly concentrated waste. Studies have focused on their kidney physiology; however investigators previously lacked the resources necessary to identify the genes underlying this adaptation. This project will use next generation sequencing to survey the kidney transcriptomes (i.e., genes expressed in the kidney) of desert adapted Heteromyids from the Southwestern United States (Dipodomys spectabilis and Chaetodipus baileyi) as well as a Heteromyid species from the rainforests of Costa Rica (Heteromys desmarestianus). The goal of this research is to identify the genetic basis of an adaptation for efficient water use by desert rodents in the family Heteromyidae. Thus, the project will identify differences in gene expression and sequence evolution between desert adapted species and a species that has evolved without the selective pressure of water scarcity. These differences will permit the identification of genes integral to efficient kidney function and water retention as well the molecular basis of adaptations to life in arid habitats. Additionally, these insights could extend our understanding of patterns of gene expression and mutations behind abnormal kidney function and kidney disease.
The goal of this project was to study the genetic basis of adaptation to desert life. Specifically, we studied the genes that were expressed in the kidneys of the banner tailed kangaroo rat, Dipodomys spectabilis and two related species, Chaetodipus baileyi and Heteromys desmarestianus. Kangaroo rat species have been studied as an example of adaptation to arid habitats because they are able to survive in these extremely dry environments without drinking water. Studies have shown that this is due to efficient kidney function and that they lose very little water during waste excretion (in other words they produce really concentrated urine). However, we do not understand the genetic basis of this efficient kidney function and this was the goal of our study. To understand the genetic basis of this adaptation we utilized new sequencing technologies to sequence the genes expressed in the kidneys of four Dipodomys spectabilis. We also sequenced the genes expressed in the kidneys of two related species, Chaetodipus baileyi and Heteromys desmarestianus. Chaetodipus baileyi is another desert species with a similar ability to concentrate urine while Heteromys desmarestianus is native to rainforest and jungle habitat in Central America where water scarcity would not be a problem. We collected D. spectabilis and C. baileyi from the same location in southeastern Arizona and collected H. demsarestianus from a mesic site in Costa Rica. We sequenced the RNA (the expressed sequence of each gene) extracted from kidneys of 4 individuals per species, which tells us what genes are turned on and how high the expression is from how much RNA we sequence from a given gene. In other words it is a proxy for how much gene product (proteins) is being produced in that tissue. We predicted that genes that are important for efficient kidney function under arid conditions would have higher expression in the two desert species (Dipodomys spectabilis and Chaetodipus baileyi) than in the rainforest species (Heteromys desmarestianus). Indeed from our work we were able to find a number of genes (over 1,400) that were expressed at higher levels in these desert species than the rainforest species. Some of these genes are genes involved in transporting salts and ions into the kidney to produce a concentration gradient that pulls water back into the body and out of what will become the urine. We are currently studying the sequence of these genes in more depth to determine if the two desert species share any characteristics that indicate they have experienced selection differently than the rainforest species. Understanding what genes are regulated for efficient kidney function is of interest because many desert species share unique kidney physiology relative to other species and a common suite of genes may be responsible for a common adaptation to desert life. Additionally, understanding kidney function in these species may help in understanding and management of human kidney diseases. In terms of broader impacts this work has led to the training of multiple undergraduate students, one of whom has since entered a graduate school program in genetics. Additionally this work has allowed the investigators to interact with local residents in Arizona as well as k-12 students near Purdue University in West Lafayette, Indiana, to explain ways in which genetics can help scientists learn about the natural world and how species can cope with extreme environmental conditions.