Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence.

理论预测，当选择对种群分化的影响从主要由作用于单个基因的直接选择效应，转变为基因组中所有受选择基因的集体特性时，存在基因流的物种形成（speciation-with-gene-flow）更易发生。因此，理解基于生态的选择（ecologically based selection）的直接影响，以及由基因座（locus，复数loci）间相关性带来的间接效应，对理解物种形成过程至关重要。本研究针对作为当代存在基因流的物种形成模型的苹果实蝇（*Rhagoletis pomonella*，双翅目：实蝇科）的山楂与苹果寄主宗（host race），量化了寄主相关选择（host-associated selection）的全基因组影响。基于寄主物候（host phenology）的选择实验所诱导的32455个单核苷酸多态性（Single Nucleotide Polymorphism，简称SNP，本文中为SNPs）的等位基因频率变化覆盖全基因组，且与自然界中共存的苹果与山楂实蝇种群间的遗传分化高度一致。苹果实蝇实验种群与自然种群间这一显著的全基因组相似性，突显了分化早期阶段生态选择的重要性，并呼吁进一步整合生态进化动力学（eco-evolutionary dynamics）与基因组分化相关研究。