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.

物种辐射演化可由种群内已存在的表型分化所促进，例如通过性别特异性发育或偏向特定生殖或营养形态的发育过程所产生的分化。我们旨在利用嗡蜣螂属（Onthophagus）的三种有角甲虫，采用比较转录组学（comparative transcriptomics）方法，检验该假说以对比种间与种内分化。这三个物种沿三个表型轴存在差异，这些轴反映了该属内绝大多数的种间多样性：角的着生位置、性二型的极性，以及营养敏感性程度。本研究方法整合了从头转录组组装、同源基因对（orthologous gene pairs）间的dN/dS（非同义替换速率与同义替换速率比值）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比值大于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比值，该类群的特征为营养多型性丧失以及性二型的反转。此外，我们发现，在我们的一个研究焦点物种中呈条件性表达（即随性别、营养或身体区域变化的表达）的基因，在沿同一形态轴（即性二型的极性、营养敏感性程度或角的着生位置）发生分化的物种类对间，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由条件特异性发育导致的种内分化，与物种类群间的遗传分化之间存在正相关关系。