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.

物种辐射演化可能因种群内已存在的表型分化而得以促进，例如通过性别特异性发育，或是偏向特定生殖或营养形态的发育过程所产生的分化。我们旨在通过比较转录组学方法，利用蜣螂属（Onthophagus）的三个角甲虫物种，检验这一假说，以对比种间及种内分化。这三个物种沿三个表型轴存在差异，这些轴反映了该属内大部分的种间多样性：角的着生位置、性二型的极性，以及营养敏感性的程度。我们的研究方法整合了从头转录组组装、同源基因对间氨基酸替换速率比（dN/dS）的评估，以及基因功能与条件性基因表达数据的整合。我们在三个物种类对中鉴定出17个与轴模式形成、发育及代谢相关的基因，其dN/dS>1；并且在亲缘关系最近的物种类对中，检测到与代谢和生物合成相关的基因具有升高的dN/dS值——该类对的特征是丧失了营养多型性，且发生了性二型的逆转。此外，我们发现，在我们的一个焦点物种内，依据性别、营养状况或身体区域条件性表达的基因，在沿同一形态轴（即性二型的极性、营养敏感性的程度，或角的着生位置）发生分化的物种类对之间，也表现出更强的正向选择或松弛纯化选择信号。因此，我们的研究结果揭示了因条件特异性发育导致的种内分化，与物种类间遗传分化之间存在正相关关系。