Keywords

Immunogenetics, genomics, habitat fragmentation

Abstract

Habitat fragmentation is a severe threat to biodiversity by reducing population size, gene flow, and adaptive potential, especially in habitat specialists like the Florida Scrub-Jay (Aphelocoma coerulescens). This dissertation integrates whole-genome sequencing and immunogenetics to assess the genomic consequences of habitat fragmentation across three primary Florida Scrub-Jay strongholds: Archbold Biological Station, Ocala National Forest, and Florida’s East Coast. In Chapter 2, I focused on adaptive genetic diversity at the Major Histocompatibility Complex (MHC) class II genes. I characterized MHC allelic richness, evaluated signatures of selection, and examined associations with pathogen infections. Despite population declines, I found moderate MHC diversity, suggesting selection helps maintain functional variation even when genome-wide diversity declines. In Chapter 3, I utilized genome-wide single nucleotide polymorphisms (SNPs) to assess population structure, gene flow, and local adaptation. Strong genetic structure of six distinct clusters were identified, including three clusters within Brevard County, matching defined metapopulations. I observed reduced genetic diversity and elevated differentiation in isolated populations like Archbold, while larger populations such as Ocala retained higher diversity. I detected loci under selection, indicating signals of local adaptation. In Chapter 4, using genome-wide SNPs and MHC data, I examined whether Florida Scrub-Jays avoid mating with close relatives or select mates based on MHC dissimilarity. While we found limited support for MHC-based mate choice, true breeding pairs were generally more related than random pairs, particularly in fragmented regions in which the populations exhibited iv higher inbreeding levels. By combining neutral and adaptive genetic perspectives, this study provides a comprehensive evaluation of fragmentation impacts on an imperiled species. Our findings highlight the importance of maintaining genetic connectivity and managing isolated populations to preserve evolutionary potential. This integrative approach informs conservation strategies aimed at enhancing the long-term viability of Florida Scrub-Jays in fragmented landscapes.

Completion Date

2025

Semester

Summer

Committee Chair

Eric A. Hoffman

Degree

Doctor of Philosophy (Ph.D.)

College

College of Sciences

Department

Biology

Format

PDF

Identifier

DP0029540

Language

English

Document Type

Thesis

Campus Location

Orlando (Main) Campus

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