Understanding Osmoregulation and Immunity in Heteromyid Rodents Through Insights Gained from RNA-Seq

Understanding the genetic basis of adaptation is one of the central questions of evolutionary genetics. In the face of selective pressure, individuals with adaptive phenotypes survive and pass on their beneficial alleles that conferred this fitness advantage. Over sufficient time scales and under strong selection, differences accumulate between taxa in the form of physical and/or behavioral traits that have been shaped differently. By looking at the transcriptomes of related taxa we can identify sequence and regulatory differences that represent molecular signatures of these different selection regimes. When we study these differences between taxa that have evolved under opposing selective forces we can identify the genetic underpinnings of adaptation to those conditions. Species from the Heteromyidae form an exemplary system for studying the genetics of adaptation in a comparative framework. This new world family of rodents is comprised of three subfamilies (the Dipodomyinae, Perognathinae, and Heteromyinae) that range from the temperate/arid habitat of the southwestern United States down through Mexico and the mesic habitat of Central America into northern South America. Members of the Dipodomyinae and Perognathinae largely populate desert habitat and have developed numerous behavioral and physiological adaptations to combat the issue of water loss. This response to selection has manifested itself in extraordinarily efficient kidney function that forms a textbook example of adaptation. However, despite knowledge of their kidney physiology, the genetic basis of this ability to retain water during waste production is unknown. In contrast to the other Heteromyids, members of the Heteromyinae largely inhabit wet tropical and subtropical forest without the same need for efficient water use. This, coupled with a near simultaneous radiation into the three subfamilies provides a controlled framework to identify differences between species from dry and wet habitat as well as between temperate and tropical species. In this dissertation I utilize 2nd generation sequencing technologies to study these differences by characterizing the genes expressed in biologically interesting tissues of three Heteromyid species. In sequencing the kidney and spleen transcriptomes of adult Dipodomys spectabilis (banner-tailed kangaroo rat), Chaetodipus baileyi (Bailey\u27s pocket mouse), and Heteromys desmarestianus (forest spiny pocket mouse), I have sampled a representative of the Dipodomyinae, Perognathinae, and Heteromyinae, respectively. In chapter 1, I took a first pass at characterizing the kidney transcriptome of D. spectabilis. I identified a priori candidate genes important to kidney function from genetic model rodent species in an effort to identify potential drivers of D. spectabilis\u27 recorded ability to retain water during the production of highly concentrated waste. I hypothesized that those candidates identified in D. spectabilis coupled with genes upregulated in this adapted organ would contain signatures of selection and have drastically divergent patterns of expression as hallmarks of their role in adaptation to a desert lifestyle. In chapter 2, I sought to identify if these or other genes exhibited clear patterns of differential expression and differentiation from the mesic H. desmarestianus that were driven by the different selective regimes on desert and mesic species. I also compared both species to C. baileyi, hypothesizing that any consistent differences seen in both C. baileyi and D. spectabilis relative to H. desmarestianus would be attributable to adaptation to arid habitat. In this chapter I identified a large number of genes in each species (roughly 11,000 per species) and filtered this set down to a subset of genes that either due to expression patterns or positive selection have evidence to be possible drivers of efficient osmoregulation in desert Heteromyids. For chapter 3, I focused on the genes expressed in spleen as an important tissue for immune response. Again I utilized the comparative framework of the Heteromyid family history in comparing the tropical H. desmarestianus to the temperate D. spectabilis and C. baileyi. My hypothesis was that greater selective pressure on immune response from increased pathogen diversity and burden in the tropics would fashion sequence evolution and different levels of gene regulation for immunity genes in H. desmarestianus. As in chapter 2, I generated a large amount of sequence data while winnowing down to a small number of solid candidate genes displaying positive selection and differential gene expression between the tropical and temperate Heteromyids. Due to the consistent patterns seen in the comparisons of D. spectabilis and C. baileyi against H. desmarestianus I predict that a subset of the genes identified here from kidney and spleen RNA-seq will prove to play a significant adaptive role in other vertebrates. Namely, the genes identified in chapters 1 and 2 will play roles in adaptation to water scarcity and those identified in chapter 3 will be consistently affected by the immune challenge of increased pathogen exposure in tropical species