UC San Diego

In the California Current upwelling system, long-term trends in ocean warming, stratification, deoxygenation, and ocean acidification are already being observed, including a shoaling of the hypoxic boundary and a decrease in calcium carbonate saturation state. The California market squid, \emph{Doryteuthis opalescens}, is a primary forage species for fish, sharks, mammals, and seabirds in the California Current, and one of California's largest fisheries. As \emph{D. opalescens} embryos are attached to the seafloor and must survive strong fluctuations in environmental conditions over development, this species may be resilient to changes in pH and oxygen and represents an ideal opportunity to investigate mechanisms of resilience to climate change in highly dynamic environments. This dissertation combines genome-wide gene expression (RNA-Seq) with hatching survival to assess the physiological response of D. opalescens embryos to low pH and low oxygen conditions and investigate potential effects of these conditions on reproductive output of the population. Chapter 2 focused on developing a high-quality, comprehensive set of expressed transcripts (‘transcriptome’) to form the basis for all downstream analyses. This chapter culminated in the development of an open-source, automated, best-practices transcriptome analysis pipeline to conduct transcriptome analyses, quality assessment, annotation, and expression analyses in a single step, available online. Chapter 3 leveraged this transcriptome to investigate the effects of low pH and low oxygen on squid development. Embryos were reared in replicate seawater tanks of ambient (control; 240 µmol/kg O2, pH 7.95) and low-pH, low-O2 (low pHOx; 90 µmol/kg O2, pH 7.55) until hatching. These conditions represent the limits of pHOx observed in squid spawning habitat. Embryos exposed to low pHOx conditions experienced a 11.8\% increase in development time, a 4.3\% decrease in hatching success, and significantly altered gene expression of stress response, oxygen sensitive genes, as well as transcription factors known to be implicated in environmental control of developmental timing. Due to the observed increase in developmental time in response to low pHOx conditions, Chapter 4 focused on pathway-directed characterization of developmental biomarkers in D. opalescens. The expression patterns identified in this chapter lay the groundwork for enhanced understanding of developmental dynamics and resilience in this tolerant, economically important invertebrate.