Data from: High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement

Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted of adaptations that involve sets of high dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining by high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection.尽管适应性演化通常与表型的复杂变化紧密相关，但针对涉及多组高维性状的适应性演化所开展的遗传学研究仍较为匮乏。基因芯片（microarrays）可提供基因表达的高维表征，而适应性演化引发的表型变化往往伴随基因表达的大规模改变。本研究展示了如何借助经典遗传学实验设计内的高维方差分解方法，完成对适应性演化过程中产生的基因表达大规模变化的遗传学分析。本研究针对由两个因自然选择而发生分化的锯缘果蝇（Drosophila serrata）种群构建的重组自交系（recombinant inbred lines, RILs）群体开展了基因芯片实验，结果显示在所检测的3762个基因产物中，有10.6%存在遗传分化。在所检测的转录本丰度的遗传分化中，仅12个遗传模块便解释了其中超过97%的变异。其中两个最为关键的遗传模块可解释转录本丰度遗传变异的50%，且与已知受选择作用的形态性状存在遗传相关性。本研究随后在独立实验中，利用实时定量逆转录PCR（qRT-PCR）对来自这两个关键遗传模块的3个候选基因的表达量进行了检测，检测对象为该重组自交系群体中的430个个体，结果证实了转录本丰度与受选择形态性状之间的遗传关联。