Theodore E. Squires: Evolutionary ecogenomics of North Atlantic ptarmigan

Abstract

This thesis integrates a new chromosome level reference genome with population and temporal whole genome resequencing data to understand adaptation, demographic dynamics, and conservation risks for Rock Ptarmigan (Lagopus muta) in Iceland and around the North Atlantic. Paper I delivers a high quality 1.03 Gb assembly and annotation that enables robust mapping and functional interpretation. Using 99 ptarmigan genomes from nine countries, two climate products (CHELSA, WorldClim), and two statistical tools (BayPass, LEA) Paper II shows that climate associated variation is broadly polygenic and that genomic offset forecasts are highly sensitive to climate dataset and association method, yielding divergent vulnerability maps for Arctic and alpine populations. Paper III leverages 91 juvenile birds from an 11-year time series to demonstrate pervasive, rapid allele frequency oscillations aligned with multi annual population cycles; many fluctuating loci map to neurological, behavioral, and immune pathways, consistent with density dependent selection maintaining polymorphism. Paper IV reports an exploratory GWAS on 90 juveniles, finding no single large effect loci for condition traits (fat, size, weight) and supporting a highly polygenic architecture; however, plausible candidate genes (e.g., HIVEP3, HTR1F, LAMA3, GALNT9, ACSL3, EBF1) offer hypotheses for targeted follow up. Across papers the work yields practical guidance for future conservation work: prioritize ensemble climate models, expand temporal genomic monitoring, preserve functional genetic diversity, and develop regionally informed management. Together, these studies provide genomic resources, analytical workflows, and an empirically grounded framework for forecasting and managing ptarmigan populations under rapid environmental change.