The role of ancient supergenes and genomic structural variation in contemporary intra-specific biodiversity

Understanding individual-based genetic differences within wild populations is central to our understanding of biodiversity, how species form, and successful resource management. Genomic structural variation represents the largest source of inter-individual genetic variation and is defined as genomic regions that differ in copy number, orientation, or chromosomal location. Chromosomal rearrangements can capture suites of co-adapted alleles providing protection from recombination, and a source of modular standing variation facilitating the formation of complex phenotypes. The overarching theme of my research program is to examine the role of chromosomal structural variation in adaptive diversity within widely distributed and often high gene flow aquatic species. The hypothesis being examined is that adaptive differences in aquatic species that are characterized by high dispersal potential are commonly associated with existing and often ancient chromosomal structural variants that protect suits of co-adapted alleles from recombination providing a source of existing modular standing variation. Species identified for inclusion were chosen to represent a wide range of dispersal potential and levels of gene flow, and as such, a long-term goal of this program is to evaluate the association between structure variation, life history as it relates to dispersal potential and gene flow, and the formation of complex phenotypes. Specifically, the main objectives are to: 1) evaluate and develop bioinformatic and statistical solutions for detecting, and analyzing structural variation; 2) identify structural variants across the genomes of a diverse suite of marine taxa and explore their phylogenies; 3) explore associations among chromosomal structural variation and environmental, life history variation, and genome wide gene expression. Comparisons across these taxa will allow an examination of the interplay between gene flow, selection, and structural variation in the formation of complex phenotypes. Potential theoretical and applied outcomes of this work include an improved understanding of how chromosomal re-arrangements may modulate the interplay between selection, drift, and gene flow in marine species, and the identification of phenotypically linked variants or keystone supergenes which may provide unprecedented opportunity for integration into existing management and assessment paradigms.