Data from: Signals of selection in conditionally expressed genes in the diversification of three horned beetles species

Species radiations may be facilitated by phenotypic differentiation already present within populations, such as those arising through sex-specific development or developmental processes biased toward particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism, and degree of nutritional sensitivity. Our approach combined de novo transcript assembly, assessment of amino acid substitutions (dN/dS) across orthologous gene pairs, and integration of gene function and conditional gene expression data. We identified 17 genes across the three species pairs related to axis patterning, development, and metabolism with dN/dS >1 and detected elevated dN/dS in genes related to metabolism and biosynthesis in the most closely related species pair, which is characterized by a loss of nutritional polyphenism and a reversal of sexual dimorphism. Further, we found that genes that are conditionally expressed (i.e. as a function of sex, nutrition, or body region) within one of our focal species also showed significantly stronger signals of positive or relaxed purifying selection between species divergent along the same morphological axis (i.e. polarity of sexual dimorphism, degree of nutritional sensitivity, or location of horns). Our findings thus reveal a positive relationship between intraspecific differentiation due to condition-specific development and genetic divergences among species.物种辐射演化可借助种群内已存在的表型分化得以推进，例如通过性别特异性发育，或是偏向特定生殖或营养型态的发育过程所产生的表型分化。本研究以嗡蜣螂属（Onthophagus）的3个角甲虫物种为研究对象，采用比较转录组学方法，对物种间及物种内的分化进行对比分析，以此检验上述假说。这3个物种沿3个表型轴存在差异，这些差异反映了该属内大部分的种间多样性：即角的着生位置、性二态性的极性，以及营养敏感性的强弱。本研究方法整合了从头转录组组装、直系同源基因对间的氨基酸替换速率比（dN/dS）评估，以及基因功能与条件性基因表达数据的整合分析。我们在3个物种对中鉴定出17个与体轴模式建成、发育及代谢相关的基因，其dN/dS值大于1；并且在亲缘关系最近的物种对中，检测到与代谢和生物合成相关的基因具有升高的dN/dS值，该物种对的特征为营养多型性丧失以及性二态性逆转。此外，我们发现，在其中一个目标物种中呈条件性表达（即随性别、营养状况或身体部位不同而变化的表达模式）的基因，在沿相同形态轴（即性二态性的极性、营养敏感性的强弱，或角的着生位置）发生分化的物种间，也表现出更强的正选择或放松纯化选择信号。因此，本研究结果揭示了由条件特异性发育导致的种内分化与物种间遗传分化之间存在正相关关系。