The genomic basis of adaptation in threespine stickleback fish

Evolutionary biology consists in the study of the evolutionary processes responsible of the diversification and adaptation of life forms over time. When adapting to a new environment (or changes in their local environment), populations have to adapt through natural selection. Until recently, the study of adaptation was focusing on fathoming the consequences of natural selection at the phenotypic level and how phenotypic evolution is linked to genetic changes. The development of new genetic and genomic tools in the last 20 years, like high-throughput sequencing technologies, now allows the construction of reference genomes in a variety of non-model organisms and the investigation of the genomic basis of adaptation. In my thesis, I investigated the genomic basis of adaptation by exploring the consequences of natural selection at the molecular level using the threespine stickleback fish (Gasterosteus acualeatus) as a model. In more detail, my work focused on three main topics: the genomic basis of parallel adaptation to acidic versus basic lochs of North Uist (Outer Hebrides, Scotland); the maintenance of standing genetic variation in Atlantic stickleback fish, and the characterization of reproductive isolation at the genomic level between parapatric stickleback populations of the Misty watershed (Vancouver Island, British Columbia, Canada)

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Classification of Lifshitz invariant in multiband superconductors: an application to Leggett modes in the linear response regime in Kagome lattice models

Multiband superconductors are sources of rich physics arising from multiple order parameters, which show unique collective dynamics including Leggett mode as relative phase oscillations. Previously, it has been pointed out that the Leggett mode can be optically excited in the linear response regime, as demonstrated in a one-dimensional model for multiband superconductors[T. Kamatani, et al., Phys. Rev. B 105, 094520 (2022)]. Here we identify the linear coupling term in the Ginzburg-Landau free energy to be the so-called Lifshitz invariant, which takes a form of $\boldsymbol{d}\cdot\left(\Psi^{*}_{i}\nabla\Psi_{j} - \Psi_{j}\nabla\Psi^{*}_{i}\right)$, where $\boldsymbol{d}$ is a constant vector and $\Psi_{i}$ and $\Psi_{j}$ $(i\neq j)$ represent superconducting order parameters. We have classified all pairs of irreducible representations of order parameters in the crystallographic point groups that allow for the existence of the Lifshitz invariant. We emphasize that the Lifshitz invariant can appear even in systems with inversion symmetry. The results are applied to a model of $s$-wave superconductors on a Kagome lattice with various bond orders, for which in some cases we confirm that the Leggett mode appears as a resonance peak in a linear optical conductivity spectrum based on microscopic calculations. We discuss a possible experimental observation of the Leggett mode by a linear optical response in multiband superconductors.Comment: 27 pages, 6 figure

The maintenance of standing genetic variation: Gene flow vs. selective neutrality in Atlantic stickleback fish

Adaptation to derived habitats often occurs from standing genetic variation. The maintenance within ancestral populations of genetic variants favourable in derived habitats is commonly ascribed to long-term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favoured in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish (Gasterosteus aculeatus) to a rare derived habitat-nutrient-depleted acidic lakes-based on whole-genome sequence data. Sequencing marine stickleback from six locations across the Atlantic Ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic-adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of standing genetic variation, and calls for a better understanding of the fitness consequences of adaptive variation across habitats and genomic backgrounds