Date of Award

Summer 8-20-2020

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Master of Science (MS)


Marine Biology


Kristina Cammen

Second Committee Member

Pauline Kamath

Third Committee Member

Nishad Jayasundara


Gray (Halichoerus grypus) and harbor (Phoca vitulina) seals are sympatric species that inhabit the North Atlantic and have been subject to mortality events from disease outbreaks, particularly phocine distemper and avian influenza virus. Across mortality events, gray seals tend to exhibit a higher survival rate, which could be explained by various ecological factors impacting rates or direction of selection in parts of the genome related to the immune system. These factors could include haul-out site density, habitat, and degree of inter/intraspecies interaction. This research aims to compare genetic diversity within the Major Histocompatibility Complex (MHC) class I gene complex among gray and harbor seals sampled in the Northwest Atlantic to investigate how they have evolved in the face of shared natural stressors. MHC genes encode immune system receptors that recognize foreign pathogens, with class I responding to viral pathogens in particular. Possessing greater genetic diversity at MHC-I can be tied to greater immunocompetence. Due to high levels of gene duplication and polymorphism, MHC class I diversity has been traditionally challenging to evaluate at a population scale, but recent advances in sequencing technology enable high-throughput MHC genotyping. In this study, amplicon sequencing was used to characterize diversity in exons 2 and 3 of MHC-I, which encode the peptide binding region. Analyses were performed on tissue biopsy samples from harbor seals by-caught in the Northeast US (n = 30), live harbor seal pups sampled in the Gulf of St. Lawrence (n = 30), and live gray seal pups sampled in Massachusetts (n = 30), Sable Island (n = 30), and the Gulf of St. Lawrence (n = 30). I compared the total number of MHC alleles, average number of alleles per individual, and sequence diversity among populations within species, as well as between species. My findings highlight the extent of allelic diversity and gene duplication that is present in MHC-I across Northwest Atlantic pinniped populations despite historical population bottlenecks. The presence of shared alleles between species and the lack of significant differences found for comparisons intra- or inter-specific MHC-I diversity suggest a shared selection regime in the MHC-I region for harbor and gray seals in the Northwest Atlantic. Overall, this study emphasizes the value of next-generation sequencing approaches to characterize multiple MHC loci given its polymorphic and duplicated nature. As gray seal populations expand, and sympatric harbor seal populations decline, a better understanding of the role of immunogenetic diversity in gray seal disease resistance will provide important insights into their role as disease reservoirs in coastal ecosystems.