Integrating genomic, transcriptomic and developmental approaches to investigate coloniality and life cycle evolution in the Hydractiniidae (Hydrozoa: Cnidaria)

Abstract

Integrative approaches to evolutionary biology yield rich data through which we can truly begin to understand the marvels of life. This dissertation integrates genomic, transcriptomic, and developmental approaches to understand the evolution of prominent life history characters of the cnidarian class Hydrozoa, including the transition from solitary to colonial forms, an elaboration of coloniality known as polyp polymorphism, and medusae (jellyfish) evolution and loss. While these characters have been repeatedly explored phylogenetically, recognizing interesting and complex evolutionary patterns of character transitions, understanding of these complex patterns of character evolution will ultimately come from insight into their development. In this dissertation, I have developed workflows for analyzing RNA-Seq data in both an intra- and interspecific comparative context. Using next-generation sequencing I not only characterize entire transcriptomic expression profiles in various tissues of two hydractiniid hydrozoans, Hydractinia symbiolongicarpus and Podocoryna carnea, but also assess and accurately characterize intra- and interspecific changes in gene expression. Using these unbiased differential expression analyses, I identify correlated changes in expression and propose candidate genes and gene pathways that are potentially involved in these key transitions. Furthermore, using whole mount in situ hybridization to characterize the spatial expression of various candidates genes, I validated each approach showing expression consistent with their role in the development of a particular tissue or life cycle stage. Results presented in this dissertation suggest that the differential regulation of gene expression, as well as novel gene gain and loss appear to have played an important role in hydrozoan life cycle transitions. Moreover, these results reveal the power of these unbiased genomic/transcriptomic methods over traditional comparative candidate gene approaches to address longstanding questions of hydrozoan morphology and evolution.