DOI: 10.5061/dryad.7pvmcvdqx
title: PhD Thesis: Tracing Molecular Patterns of Adaptation in Arctic Brassicaceae

description: Extreme environments can function as natural laboratories for studying how
 different organisms adapt to similar selection pressures at the genetic
 level. This thesis explores how three Arctic plant species independently
 adapted to some of the coldest biomes on Earth, and how they evolved
 similar suites of adaptations to extremes in light and temperature. It
 addresses fundamental questions in plant evolutionary biology, such as the
 extent to which adaptation follows the same genetic trajectories in
 different species, and the genetic basis for plant adaptation to extreme
 environments. The thesis has two main objectives that are addressed
 through three papers (Papers I-III): 1) estimate the degree of adaptive
 molecular convergence in the three Arctic Brassicaceae Cardamine
 bellidifolia, Cochlearia groenlandica, and Draba nivalis, and 2) identify
 putative molecular adaptations to the Arctic environment in the same three
 species. Approach. The first two papers examine the degree of evolutionary
 repeatability in how C. bellidifolia, C. groenlandica, and D. nivalis
 adapted to the Arctic environment at the genetic level (objective 1). In
 Paper I, we estimated molecular convergence at the level of codons, genes,
 and functional pathways, by comparing genome-wide patterns of positive
 selection and identifying convergent substitutions in the three species.
 In Paper II, we conducted a time series experiment to examine the
 transcriptional responses of the Arctic Brassicaceae to low temperatures,
 and to identify potential convergent expression patterns in cold response.
 All three papers identify putative molecular adaptations to extremes in
 light and temperature (objective 2). In Paper I, we identified candidate
 genes for adaptation to the Arctic environment by searching for positively
 selected genes associated with abiotic stresses common in the Arctic. In
 Paper II, we explored the molecular basis of cold tolerance in Arctic
 Brassicaceae, and described how their cold-induced transcriptomes differ
 from that of the temperate model species, Arabidopsis thaliana. In Paper
 III, we assembled the genome of D. nivalis and explored the genomic
 characteristics of Arctic plant adaptation, by conducting comparative
 analyses of chromosomal evolution and functional genomics with other
 species in the Brassicaceae. Main findings and discussion. The findings in
 Papers I-II suggests that the three Arctic Brassicaceae have adapted to
 the Arctic environment through independent genetic trajectories (objective
 1). In Paper I, we found that positive selection has been acting on
 different genes, but similar functional pathways in the three species. The
 positively selected genes sets showed convergent functional profiles
 associated with abiotic stresses common in the Arctic. However, we found
 little evidence for convergent substitutions at the same sites, or for
 positive selection acting on the same genes in the three species. In Paper
 II, we found that the cold-response of C. bellidifolia, C. groenlandica,
 and D. nivalis was highly species-specific. Most cold-induced genes were
 unique for each species, and the number of genes shared by the three
 Arctic species and the temperate A. thaliana was higher than the number of
 genes shared by the Arctic species alone. This suggests that the cold
 response in Arctic Brassicaceae mainly evolved independently, but with
 some components likely conserved across the family. The low levels of
 molecular convergence could be explained by the many evolutionary
 trajectories leading to better performance under temperature and light
 stress in plants, and/or less repeatable patterns of adaptation in highly
 polygenic traits such as cold tolerance. Papers I-III presents some of the
 first molecular evidence for putative plant adaptations to the Arctic
 environment (objective 2). In Paper I, we found multiple candidate genes
 for Arctic adaptation associated with cold stress, freezing stress,
 oxidative stress and light stress in all species. Adaptations associated
 with the plasma membrane seemed to be particularly important in all
 species, possibly due to its crucial role in freezing tolerance. In Paper
 II, we found that the Arctic cold response followed similar trends as in
 the temperate A. thaliana, but a few genes and characteristics were
 specific for the Arctic species alone. In Paper III, we presented a 302 Mb
 assembly of D. nivalis that is highly contiguous with 91.6 % assembled
 into eight chromosomes (the base chromosome of the species). We found that
 the D. nivalis genome contains expanded suites of genes associated with
 common Arctic stresses, and the expansion of these gene families appear to
 partly be driven by the activity of transposable elements. Conclusion. The
 results from this dissertation provide a framework for studies that aim to
 test the existence of a functional syndrome of Arctic adaptation in
 Brassicaceae and other flowering plants. The D. nivalis genome assembly
 may also become an important tool in studies of Arctic plant evolution in
 general.