Shafer, Aaron B A

The diversification of mammals has been shaped by climatic fluctuations and geological changes over millions of years. Among them, shrews (Soricidae) stand out as one of the most diverse mammalian lineages. Shrews are found on most continents and have evolved remarkable adaptations at the species and population levels. Although evolutionary studies of shrews have been limited by a lack of genomic resources, this work aimed to address this gap by developing such resources and using various omics approaches to explore adaptation and divergence in shrews, with a particular focus on an isolated population on Bon Portage Island (BPI), Nova Scotia, Canada. BPI shrews exhibit distinctive foraging habits and possess a unique allele for a dietary enzyme, which may represent an adaptation to their specialized diet. My research involved assembling and annotating de novo genomes from three shrew species. In Chapter 2 I conducted a comparative genomic analysis of 20 mammals (including four shrew species) to identify lineage-specific adaptations including accelerated regions, gene family expansions, and positively selected genes. I found shrew-specific variants in genes associated with the nervous, metabolic, and auditory systems, which may underlie some of their unique traits. In Chapter 3, I examined morphological and epigenetic divergence between mainland and island populations of masked shrews (Sorex cinereus), including BPI. Island shrews exhibited smaller body sizes and signs of accelerated biological aging, marked by DNA methylation differences enriched in developmental and digestive pathways. Chapter 4 focused on analyzing genome-wide SNP data to identify regions of differentiation, alongside RNA-seq data to perform a differential gene expression analysis between BPI shrews and other populations. The results from both analyses revealed patterns of differentiation in genes associated with fatty acid metabolism and metabolic regulation that are likely linked to their specialized, largely marine-based diet. Additionally, I reconstructed the demographic history of Nova Scotia masked shrew populations, revealing that the divergence of the BPI population appears to coincide with rising sea levels following the last glacial maximum. These findings shed light on mechanisms of adaptation and divergence, illustrating how ecological pressures, geographic isolation, and dietary specialization shape genomic, epigenomic, and transcriptomic landscapes.

Author Keywords: comparative genomics, epigenetics, genome assembly, island syndrome, population genomics, transcriptomics