Genomics approaches to uncovering eco-evolutionary adaptations in pinnipeds

Ecological and environmental drivers shape evolution, yet little is known about the molecular underpinnings of adaptation. Omics tools (e.g. genomics and transcriptomics) can help us understand the mechanisms of long-term trait evolution, such as lactation strategies, and shorter-term population dynamics. Pinnipeds (seals, sea lions, fur seals, and walruses), a closely related monophyletic group, represent some of the most extreme and diverse lactation strategies known. This trait diversity stems from their worldwide distribution across a wide range of habitats and latitudes, and their obligate spatiotemporal separation of land and sea for breeding and foraging. In this thesis, we uncover signals of molecular evolution of key lactation traits in pinnipeds using comparative functional genomics and comparative transcriptomics. We identify candidate changes in pathways linked to mammary involution and lipid metabolism, and reveal coordinated expression of genes involved in lipid mobilisation, energy balance, high fat milk, and mother-to-pup energy transfer. Novel grey seal transcriptomes for milk fat, blubber, and pup blubber were generated from collections made in early (day 5) and late (day 15) lactation on the Isle of May 2023. Along with uncovering the protein properties of key milk fat globule membrane genes, we obtained the first physical properties of milk fat globules in grey seals – allowing us to investigate mechanisms of milk emulsion stability in high fat milk. Our findings show that seal milk contains exceptionally small globules with weakened net surface charge, offering a potential mechanism for stabilising high-fat milk. Finally, we reconstructed the demographic history and genetic health of Caspian seals, showing that changes in effective population size track major paleoenvironmental shifts while recent inbreeding remains low, providing direction for future conservation strategies. Overall, the findings presented in this thesis represent an important foundation for future omics studies targeting marine mammal biology, and offer a lens into understanding eco-evolutionary trajectories of populations and extreme phenotypes.