UC Berkeley

Understanding the genomic architecture of complex adaptive traits in natural populations has long been a central goal in evolutionary biology. Of particular interest is the extent of the “genetic toolbox,” that is: how many evolutionarily viable solutions are there to a common evolutionary problem? To get at this question, I looked at convergent adaptation to desert environments across the order Rodentia. In mammals, the problem of living in an extremely arid environment with limited access to free water has been solved in a variety of different ways. For granivorous desert rodents, many have developed ultra-efficient osmoregulatory systems, including highly modified kidneys, to handle the problem of salt and water homeostasis. Here, I examined the genomic basis of adaptation across multiple evolutionary timescales.

In chapter one, I studied the recent invasion of a North American desert by the house mouse, Mus musculus. I compared this desert population with a non-desert population and examined organismal phenotypes and gene expression profiles in the lab for experimentally dehydrated mice and for control mice. I discovered significant differences in the response to water stress in these two populations. Mice derived from a desert population showed a less extreme response to water stress, suggesting they may have adapted to live in deserts. Non-desert mice showed shifts towards desert-like gene expression after water stress, consistent with adaptive plasticity. Further, I identified candidate genes underlying desert adaptation in this population.

In chapter two, I leveraged three phylogenetically distinct species pairs, one a desert specialist and the other a mesic representative, from three families of rodents over ~70 million years of divergence and found convergent patterns of evolution using sequences of expressed genes (RNA-seq data). First, I looked for convergent shifts in gene expression associated with desert living in each species pair and identified genes displaying this pattern. Next I used multiple methods to test for aspects of convergence at the DNA sequence level and found that few genes showed both convergence in DNA expression and convergence in protein structure. I found that a greater proportion of genes tested show convergent patterns in gene expression suggesting that changes in the regulation of genes may have a greater impact than changes in protein structure during adaptation to desert environments.

In chapter three, I sequenced and assembled de novo the genome of the rock pocket mouse, Chaetodipus intermedius (Heteromyidae) using MaSuRCA. This species, found in the Sonoran and Chihuahuan deserts of North America, is a desert specialist and a model for understanding the genetics of coat color variation in wild populations. This genome is a resource to be used to further understand the genomics of adaptation in this unique lineage.