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Abstract

Arctic ecosystems are undergoing rapid warming (four times faster than the global average), forcing organisms to respond through migration, adaptation, plasticity and/or extinction. In this thesis, I use genomic approaches to understand these dynamics. I infer Arctic plant species’ historic refugia during the Pleistocene glaciations (migration), compare their genomes to determine if their shared phenotypic traits have a consistent genomic origin (adaptation), and explore their short-term genomic responses to multiple decades of experimental warming (plasticity). Using plants from 36 circumpolar, present-day populations of Cassiope tetragona, and from two Little-Ice-Age populations preserved in glaciers (250-500 years old), I determined that C. tetragona had Pleistocene glacial refugia in Alaska, Siberia, and Europe. This was the first circumpolar study of an Arctic plant to use next generation sequencing data and demographic models. Next, I built a chromosome-level genome assembly for Oxyria digyna, an ecologically well-studied, Arctic forb. Using comparative genomics with three other Arctic plant genomes and several non-Arctic species across three plant families, I found that expanded and contracted gene families in Arctic species are rarely shared across plant families but fall into similar functional categories. To explore short term genomic responses to warming, I organized the collection of tissue and seed from 102 Dryas spp. individuals. Half were from experimentally warmed plots and half from nearby control plots, at sites across the Arctic (Alaska, Northern Sweden, Svalbard, Nunavut). I analyzed the DNA methylation and gene expression of these individuals and found multiple differentially methylated regions in Low Arctic but not High Arctic sites. About 10% of genes nearby differentially methylated regions show changes in gene expression. Differentially methylated and expressed genes were consistently enriched for gene ontology terms associated with biotic interactions, but genes associated with these functions also had highly variable methylation in general. In the last chapter, I built a software package in R to identify repetitive features of chromosomes, such as putative centromeres, which I used to identify putative Arctic plant centromeres. My dissertation provides a preliminary understanding of Arctic plant genomes, their glacial refugia, current adaptations to their extreme environment, and potential future responses to warmer climates.