The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (F_ST = 0.11–0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.

中文翻译：

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北极红点鲑（Salvelinus alpinus）变种深水适应的基因组基础

北极夏尔（Salvelinus alpinus）在加拿大纽芬兰的甘德湖的冰川后殖民为研究适应极端深水环境的基因组基础提供了机会。深水 (> 50 m) 栖息地的殖民化通常需要广泛适应以应对来自高静水压力、低温和低光的新环境挑战，但这些环境中进化的基因组机制鲜为人知。在这里，我们比较了适应高达 288 m 深度的深水变种和占据较浅深度的较大的食鱼中上层变种之间的基因组差异。使用 SNP 阵列和整个核和线粒体基因组的重测序，我们发现明显的遗传差异 ( F _ST = 0.11–0.15）在深水和浅水形态之间，尽管线粒体基因组中没有形态差异。异常值分析确定了许多不同的基因组区域，这些区域包含富含基因表达和 DNA 修复、心脏功能和膜转运等过程的基因。对假定拷贝数变异 (CNV) 的检测发现了 385 个具有不同于鱼食性变体的 CNV 的基因和 275 个具有不同于深水变体的 CNV 的基因，这些基因丰富了与突触组装相关的过程。人口统计学分析确定了近期和局部形态差异的证据，以及与冰后殖民化一致的多样性持续减少。一起，