Evolution of an Adaptive Trait: Phenotypic, Physiological, and Genetic Patterns of TTX Resistance in the Sierra Garter Snake Thamnophis couchii

Understanding the molecular evolution of adaptive traits is central to advancing evolutionary biology. Thus, describing the genetic architecture of such traits is necessary to understand how adaptations arise, spread, and fix across populations. Where exactly these adaptive traits originate in the underlying genetic architecture remains a topic of controversy, with some evolutionary biologists arguing that origination of adaptive phenotypes occurs from changes in regulatory non-protein coding regions of the genome, while others claim they stem from structural mutations in protein coding regions. Complex phenotypes such as adaptations are inherently difficult to study, typically involving multiple, potentially independent, genetic mechanisms that can be challenging to recognize. Therefore, the best approach to understanding these complex phenotypes is a layered approach, examining the connection between genotypes and phenotype at many levels. Here, we examine the complex phenotype, tetrodotoxin (TTX) resistance, at multiple scales (whole animal, physiological, and genetic), hoping to uncover both structural and regulatory changes responsible for this adaptation. TTX resistance is an adaptive trait found in garter snakes (Thamnophis) that prey on toxic newts (Taricha spp.). Newts are defended by this lethal toxin (TTX) which binds to sodium channels, halts nerve impulses, and can end in death for those who ingest it. Nevertheless, some garter snake species have evolved resistance to TTX, and prey on these newts. We examined an unstudied predator-prey interaction between toxic newts and a recently discovered TTX-resistant predator, the Sierra garter snake (Th. couchii). We quantified phenotypic variation at the whole animal scale in both predator (resistance) and prey (toxicity), identifying strong trait matching at sympatric sites, and high levels of phenotypic variation in predator TTX resistance both within and among populations. We then investigated whether this variation in predator traits is explained by the same physiological and genetic mechanisms underlying predator resistance in other Thamnophis-Taricha systems. We confirmed that there is indeed a correlation between whole animal and skeletal muscle resistance and then sequenced three candidate genes and found that all individuals across the range of Th. couchii are fixed for resistance-conferring alleles despite phenotypic variation at both the whole animal and skeletal muscle levels. In the absence of structural variation in the sodium channel targets of TTX, we investigated a potential avenue for TTX resistance from a transcriptomics perspective, exploring the role of gene expression in adaptive evolution. We found over 200 differentially expressed genes among low and high resistance snakes. This body of work examines the connections between genetic mechanisms and phenotype to better understand adaptive evolution and the potential molecular constraints that act upon it