| Summary: | Understanding the reasons why intraspecific diversity arises and how populations adapt to spatial variation in environmental conditions continues to be a major focus of evolutionary biology. Recently, inversion polymorphisms have become an active area of research focused on understanding how sympatric, local adaptation occurs especially when adaptation occurs at microgeographic scales (i.e., below the scale of gene flow). However, we are still lacking a comprehensive understanding of the conditions (e.g, strength of selection, migration rate, architecture of the evolving trait) needed for inversions to facilitate local adaptation, the traits underlying adaptation, and how well we can detect them empirically. To address these gaps, my dissertation takes three distinct, but complementary approaches to understanding adaptation below the scale of gene flow in my study species Atlantic cod (Gadus morhua). Atlantic cod in the US Gulf of Maine (GOM) and Iceland harbor putative ecotypes (i.e., coastal, stationary cod and offshore, migratory cod), but we have limited genomic and phenotypic understanding for how they have evolved in these regions. To assess this, Chapter 2 is an empirical assessment of population genomic structure using high-resolution whole genome sequencing and phenotypic differentiation using body morphometric analyses. I show that although fine-scale population structure may be present between locations within the GOM, inversion haplotypes are not segregating (meaning present as uninverted in one group and as inverted in the other) between putative ecotypes (i.e., GOM color morphs) and morphological data suggest a lack of a migratory body shape in the GOM. In Iceland, however, inversions underlying ecotype differences do segregate and correspond with a more streamlined body shape found in offshore ecotypes compared to coastal ecotypes. When comparing across locations, GOM cod showed both body shape variation and inversion haplotype structure that was more closely related to coastal Icelandic cod ...
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