Gene copy number variation across individuals has been shown to track population structure and be a source of adaptive genetic variation with significant fitness impacts. In this study, we report opposite results for both predictions based on the analysis of gene copy number variants (CNVs) of Suillus brevipes, a mycorrhizal fungus adapted to coastal and montane habitats in California. In order to assess whether gene copy number variation mirrored population structure and selection in this species, we investigated two previously studied locally adapted populations showing a highly differentiated genomic region encompassing a gene predicted to confer salt tolerance. In addition, we examined whether copy number in the genes related to salt homeostasis was differentiated between the two populations. Although we found many instances of CNV regions across the genomes of S. brevipes individuals, we also found CNVs did not recover population structure and known salt-tolerance-related genes were not under selection across the coastal population. Our results contrast with predictions of CNVs matching single-nucleotide polymorphism divergence and showed CNVs of genes for salt homeostasis are not under selection in S. brevipes.

个体间的基因拷贝数变异已显示出可追踪种群结构，并且是适应性遗传变异的来源，对适应性有重大影响。在这项研究中，我们报告了两个预测的相反结果，这是基于短牛肝菌的基因拷贝数变异（CNV）的分析，一种适合加州沿海和山区栖息地的菌根真菌。为了评估基因拷贝数变化是否反映了该物种的种群结构和选择，我们调查了两个先前研究过的局部适应种群，这些种群显示了一个高度分化的基因组区域，其中包含一个预计赋予耐盐性的基因。此外，我们检查了与盐稳态相关的基因中的拷贝数是否在两个人群之间有所区别。尽管我们在短链酿酒酵母的基因组中发现了许多CNV区域实例对于个体，我们还发现CNV不能恢复种群结构，并且沿海沿海人群中未选择已知的耐盐相关基因。我们的结果与CNV匹配单核苷酸多态性差异的预测相反，并显示盐稳定状态基因的CNV不在短链酵母中选择。