Understanding genome-wide responses to environmental conditions during embryogenesis is essential for discerning the evolution of developmental plasticity and canalization, two processes generating phenotypic variation targeted by natural selection. One case of developmental plasticity is environmental sex determination (ESD) where environmental cues (such as temperature) during development direct gonadal phenotype. Sex determination can also be canalized (such as with sex chromosomes) where genetic signals instead direct development. Intriguingly, sex determination has evolved repeatedly in vertebrates, and numerous lineages often make use of similar gene players. However, the full genetic architecture of vertebrate sexual development is unknown. Emerging evidence indicates changes have occurred in both up- and downstream factors of sexual development networks. Additionally, studies point to key roles for epigenomic regulation in integrating environmental signals during development.
These elements of conservation despite sex determination diversity are fascinating, thus this dissertation asks, what changes in the genetic wiring can explain this simultaneous mechanistic diversification alongside genetic and developmental conservation? Additionally, as this turnover is associated with transitions between ESD and GSD we ask, how and when are environmental signals communicated into genetic and developmental signals and how are they ignored when environmental sensitivity is lost? A comparative perspective of turtle lineages (where sex determination has evolved repeatedly) allows contrast of proxy-ancestral temperature-dependent sex determination (TSD, Chrysemys picta) to derived GSD (Apalone spinifera, ZZ/ZW sex chromosomes). Over three studies we focused on changes in gene expression, gene regulation, and genomic environmental sensitivity to learn how environmental signals integrate into the genome (or not) during development and how developmental plasticity and canalization contribute to biodiversity.
This dissertation significantly expanded the genomic resources available for turtles and implemented novel application of multiple methodological approaches that facilitated deeper synthesis and interpretation of these resources. Among the significant findings revealed were the retention of substantial transcriptomic thermal plasticity in GSD turtles that has persisted >145 Myr since the evolution of sex chromosomes, representing plasticity in GSD species that may be co-opted during future adaptive shifts. Additionally, this dissertation expanded molecular models of sex determination through the identification of the primary cilium as a likely critical organelle involved in the sensing and integration of environmental cues during sexual development that may co-evolve with sex determination. Finally, it was the first to attempt genome-wide chromatin studies in turtles, which revealed the presence of bivalent domains that may contribute to establishing the bipotential state of the early gonad.
This dissertation has expanded our understanding of the molecular mechanisms underlying vertebrate sex determination and provides a rich source of novel observations to drive future studies in this area. This research sheds light on the gene expression, gene regulation, and environmental sensitivity that not only underly these mechanisms of sex determination but also reveal how these mechanisms evolved contributing to the vast biodiversity in sex determination observed throughout vertebrates
