Local adaptation and the evolution of genome architecture in threespine stickleback

Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these “genomic islands” is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly ...理论预测，局部适应应会推动集中型遗传架构的演化：驱动适应性分化的等位基因在染色体上呈紧密聚集状态。三刺鱼对海洋与淡水环境的适应所形成的遗传架构便与该预测相符：种群间的分化主要由少数基因组区域驱动，这些区域包含多个与环境适应性状相关的数量性状基因座（quantitative trait loci, QTL），以及具有明确表型效应的候选基因。针对这些"基因组岛"的演化，有理论提出染色体重组会重塑基因组，使因果基因座紧密相邻，但该假说尚未得到专门研究。我们借助同线性分析，识别三刺鱼基因组中的微重组与宏重组事件，并评估其在基因组岛演化中可能发挥的作用。为了鉴定染色体重组，我们开展了从头组装……