Genomic Consequences of Habitat Fragmentation in the Florida Scrub-Jay: Diversity, Adaptation, and Disease Susceptibility

Habitat fragmentation threatens biodiversity by reducing genetic diversity, limiting adaptation, and increasing inbreeding. My dissertation investigates these impacts on the Florida Scrub-Jay, a threatened, non-migratory bird endemic to Florida. Using whole-genome sequencing and immunogenetics, I examined three main strongholds (East Coast, Ocala, Archbold) to assess genetic diversity, population structure, local adaptation, and inbreeding. I first characterized
diversity and selection at immune genes (MHC), finding moderate MHC variation despite overall genetic decline. Next, I analyzed genome-wide SNPs to reveal strong genetic structure and increased differentiation in isolated populations, alongside signs of local adaptation. Finally, I examined inbreeding patterns and mate choice, not finding evidence of inbreeding avoidance, and isolated populations exhibited higher inbreeding levels, indicated by longer runs of homozygosity. This work provides critical insights for conservation management, emphasizing the need to maintain habitat connectivity and genetic diversity to support species' long-term survival. 

Maryam Ghoojaei
Dr. Eric Hoffman, Advisor