Developmental polyphenism, the ability to switch between phenotypes in response to environmental variation, involves the alternating activation of environmentally sensitive genes. Consequently, to understand how a polyphenic response evolves requires a comparative analysis of the components that make up environmentally sensitive networks. Here, we inferred co-expression networks for a morphological polyphenism, the feeding-structure dimorphism of the nematode Pristionchus pacificus. In this species, individuals produce alternative forms of a novel trait—moveable teeth, which in one morph enable predatory feeding—in response to environmental cues. To identify the origins of polyphenism network components, we independently inferred co-expression modules for more conserved transcriptional responses, including in an ancestrally non-polyphenic nematode species. Further, through genome-wide analyses of these components across the nematode family (Diplogastridae) in which the polyphenism arose, we reconstructed how network components have changed. To achieve this, we assembled and resolved the phylogenetic context for five genomes of species representing the breadth of Diplogastridae and a hypothesized outgroup. We found that gene networks instructing alternative forms arose from ancestral plastic responses to environment, specifically starvation-induced metabolism and the formation of a conserved diapause (dauer) stage. Moreover, loci from rapidly evolving gene families were integrated into these networks with higher connectivity than throughout the rest of the P. pacificus transcriptome. In summary, we show that the modular regulatory outputs of a polyphenic response evolved through the integration of conserved plastic responses into networks with genes of high evolutionary turnover.

中文翻译：

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一种新性状的多态性将快速进化的基因整合到祖先可塑性网络中。

发育多态性是响应环境变化而在表型之间切换的能力，涉及环境敏感基因的交替激活。因此，要了解多态响应如何演变，需要对构成环境敏感网络的组件进行比较分析。在这里，我们推导了共表达网络的形态学多态性，即线虫Pristionchus pacificus的进食结构二态性。在这个物种中，个体会根据环境提示产生替代形式的新特征-可移动的牙齿，可移动的牙齿以一种变体实现掠食性觅食。为了确定多态性网络组件的起源，我们独立地推断了共表达模块以获得更保守的转录反应，包括祖先的非多态线虫物种。此外，通过对产生多态性的线虫科（Diplogastridae）中这些成分的全基因组分析，我们重构了网络成分的变化方式。为实现这一目标，我们组装并解决了代表迪氏梭菌科广度和假设外种群的五个物种基因组的系统发育背景。我们发现，指示替代形式的基因网络是由祖先对环境的塑性反应引起的，特别是饥饿引起的新陈代谢和保守的滞育（dauer）阶段的形成。此外，来自快速发展的基因家族的基因座以比整个其余基因更高的连通性被整合到这些网络中。太平洋假单胞菌转录组。总而言之，我们表明，通过将保守的塑性反应整合到具有高进化周转基因的网络中，多态反应的模块化调控输出得以进化。