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

了解野生种群中基于个体的遗传差异对于我们理解生物多样性、物种如何形成和成功的资源管理至关重要。基因组结构变异是个体间遗传变异的最大来源，被定义为在拷贝数、方向或染色体位置上不同的基因组区域。染色体重排可以捕获提供重组保护的共适应等位基因组，并为形成复杂的表型提供模块化站立变异的来源。我的研究计划的首要主题是研究染色体结构变异在广泛分布且通常高基因流动的水生物种适应多样性中的作用。正在检验的假设是，具有高扩散潜力的水生物种的适应性差异通常与现有的、通常是古老的染色体结构变异有关，这些染色体结构变异保护共适应等位基因的组合，防止重组提供现有的模块化站立变异的来源。被确定为包括的物种被选择来代表广泛的扩散潜力和基因流动的水平，因此，该计划的一个长期目标是评估结构变异、与扩散潜力和基因流动有关的生活史之间的密切联系，以及复杂表型的形成。具体地说，主要目标是：1)评估和开发用于检测和分析结构变异的生物信息学和统计学解决方案；2)识别不同海洋类群基因组中的结构变异，并探索它们的系统发育；3)探索染色体结构变异与环境、生活史变异和全基因组基因表达之间的联系。通过对这些分类群的进一步比较，将能够检验基因流、选择和结构变异在复杂表型形成中的相互作用。这项工作的潜在理论和应用成果包括：更好地理解染色体重排如何调节海洋物种中选择、漂移和基因流之间的相互作用；以及识别表型连锁的变异或关键超基因，这可能为整合到现有的管理和评估范式中提供前所未有的机会。

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.