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（phenotype）的复杂变化紧密关联，但针对涉及高维性状集合的适应性演化，迄今开展的遗传学研究仍较为有限。基因芯片（Microarray）技术可获取基因表达（gene expression）的高维表征数据，而适应性演化所引发的表型变化往往会伴随基因表达的大规模改变。本研究阐明了如何通过经典遗传学实验设计中的高维方差分解（high-dimensional variance partitioning）方法，对适应性演化过程中产生的基因表达大规模变化开展遗传学分析。研究团队以两个因自然选择而发生分化的锯缘果蝇（Drosophila serrata）种群杂交得到的重组自交系（recombinant inbred lines, RILs）群体为材料开展基因芯片实验，结果显示，在检测的3762个基因产物中，有10.6%存在遗传分化。在转录本丰度（transcript abundance）的遗传分化中，超过97%的变异仅由12个遗传模块（genetic modules）所解释。其中两个最为关键的模块可解释转录本丰度50%的遗传变异，且与已知受选择作用的形态性状（morphological traits）存在遗传相关性。研究团队随后针对这两个关键遗传模块中的3个候选基因，利用实时定量聚合酶链式反应（qRT-PCR）技术对该重组自交系群体中的430个个体开展独立实验以检测其表达量，最终验证了转录本丰度与受选择形态性状之间的遗传关联。