Exploring molecular mechanisms influencing rapid adaptation and development in spring and fall Atlantic Herring (Clupea harengus)

Abstract

Adaptation is a key evolutionary process by which organisms develop increased fitness in response to a change in their habitat. In marine fishes, understanding adaptation is critical for predicting how species respond to changing ocean conditions, providing insights into evolutionary biology and informing management decisions. My thesis focuses on Atlantic Herring (Clupea harengus L.), a species of immense ecological and economic importance, to explore the mechanisms and implications of adaptation in early life stages through genetic, epigenetic, and transcriptomic analyses. I first employed a suite of microsatellite markers to explore connectivity in herring through kinship structure in Gulf of St. Lawrence Spring herring and found half-sibs and potential full-sibs in a single juvenile aggregation. This is potential evidence for kinship recognition and larval retention in a herring spawning aggregation at least six months after hatching, shedding light on the genetic structure and relationship within an aggregation. I then designed a rearing experiment to assess how temperature (11°C and 13°C) and photoperiod (6 and 12 hours daylight) influence the epigenetic and transcriptomic patterns throughout larval development. In addition to high levels of global methylation levels across all samples, a decline in global methylation level was observed with increased developmental stages and was more pronounced in the 13°C treatment. Differentially methylated sites were found primarily in exon and promoter regions of genes linked to metabolism and development. These results suggest DNA methylation is an important mechanism in herring larval development and a key component to early-stage responses to environmental stressors. Alongside the epigenetic results, I found significant differential gene expression in both environmental treatments across all developmental stages but the effects on genes were stage specific. Genes associated with eye structure constituents were upregulated in longer photoperiod treatments, and immune response associated genes were upregulated in higher temperature treatments. The transcriptomic results provide novel findings into molecular mechanisms underlying herring larval development and early life-stage response to environmental stressors. This research contributes to our understanding of how populations can rapidly adjust to changing environments and highlights the complex interplay between genetics, epigenetics, and gene expression in shaping the evolutionary trajectories of natural populations.