Search for Selection: Genomic, Transcriptomic, and Phenotypic Investigations of Spotted Seatrout (Cynoscion nebulosus)
Doctor of Philosophy (Ph.D.)
Virginia Institute of Marine Science
Richard W Brill
Kimberly S Reece
Eric J Hilton
Christine N Meynard
Climate change has resulted in both increased mean water temperature and higher frequencies of extreme water temperatures in coastal areas. These new thermal regimes exert strong selective pressure on the thermal physiology of coastal aquatic species. Phenotypic plasticity (the ability of one genotype to display multiple phenotypes) and local adaptation (increased fitness to local environment due to natural selection) dictate both short-term (from hours to days to weeks) and long-term (from years to decades) resilience of a species. To better predict how a species will respond to the negative impacts of climate change, one first needs to know the current levels of variation in plasticity and local adaptation. Marginal populations are especially critical for the persistence of a species, as those populations can harbor unique genetic variation and the interaction between plasticity and local adaptation determines the boundaries of future distributional ranges. This dissertation focuses on the northern marginal population of spotted seatrout (Cynoscion nebulosus), an estuarine-dependent fish, and compares them with those from the core region of the distribution to elucidate the physiological, transcriptomic and genetic mechanisms of plasticity and adaptation. I discovered significant differences between fish from different areas at all three levels of biological organization: Chapter 1 shows different whole-organism metabolic physiology of fish sampled from distinct populations and the northern population is consistent with cold-adaptation, given the pressure of natural selection from more severe and frequent winter kills in the region. Chapter 2 presents functional genetic evidence that the cold-adapted northern spotted seatrout are more vulnerable to heat stress than the warm-adapted southern spotted seatrout, suggesting that differential gene expression is contributing to observed differences in thermal tolerance. A liver transcriptome is de novo assembled and serves as a valuable resource for future genetic studies of spotted seatrout. Chapter 3 discovers signatures of selection based on over 15,000 genome-wide single nucleotide polymorphism (SNP) markers. The pattern of genetic variation is consistent with thermal adaptation along the US east coast. Genes involved in metabolic pathways and transcriptional regulation are the main targets of natural selection. In summary, spotted seatrout are relatively resilient to the thermal effects of climate change due to a wide range of metabolic plasticity and adaptive potential in climate-related genetic variation. Range expansion at the leading edge, however, is largely constrained by the species’ cold tolerance limit. The northern and southern population will likely respond to climate change differently and this should be taken into consideration in future conservation management of this species.
© The Author
Song, Jingwei, "Search for Selection: Genomic, Transcriptomic, and Phenotypic Investigations of Spotted Seatrout (Cynoscion nebulosus)" (2020). Dissertations, Theses, and Masters Projects. William & Mary. Paper 1681950282.