Data from: Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish

Phenotypic plasticity is the ability of organisms with a given genotype to develop different phenotypes according to environmental stimuli, resulting in individuals that are better adapted to local conditions. In spite of their ecological importance, the developmental regulatory networks underlying plastic phenotypes often remain uncharacterized. We examined the regulatory basis of diet-induced plasticity in the lower pharyngeal jaw (LPJ) of the cichlid fish Astatoreochromis alluaudi, a model species in the study of adaptive plasticity. Through raising juvenile A. alluaudi on either a hard or soft diet (hard shelled or pulverized snails) for between one and eight months, we gained insight into the temporal regulation of 19 previously identified candidate genes during the early stages of plasticity development. Plasticity in LPJ morphology was first detected between three and five months of diet treatment. The candidate genes, belonging to various functional categories, displayed dynamic expression patterns that consistently preceded the onset of morphological divergence and putatively contribute to the initiation of the plastic phenotypes. Within functional categories we observed striking co-expression, and transcription factor binding site analysis was used to examine the prospective basis of their co-regulation. We propose a regulatory network of LPJ plasticity in cichlids, presenting evidence for regulatory cross-talk between bone and muscle tissues, which putatively facilitates the development of this highly integrated trait. Through incorporating a developmental time-course into a phenotypic plasticity study, we have identified an interconnected, environmentally responsive regulatory network that shapes the development of plasticity in a key innovation of East African cichlids.

表型可塑性（Phenotypic plasticity）指携带特定基因型的生物体依据环境刺激发育出不同表型的能力，最终使个体更适应当地环境。尽管其在生态系统中具有重要意义，但塑性表型背后的发育调控网络往往仍未被解析。我们以慈鲷鱼类阿氏异齿非鲫（Astatoreochromis alluaudi）——适应性可塑性研究中的模式物种——的下咽骨（lower pharyngeal jaw, LPJ）为研究对象，探究饮食诱导的可塑性的调控基础。通过将幼年期阿氏异齿非鲫分别投喂硬食（带壳螺类）或软食（粉碎螺类）长达1至8个月，我们解析了19个已报道的候选基因在可塑性发育早期的时序调控模式。LPJ形态的可塑性首次在投喂饮食3至5个月间被检测到。隶属于多个功能类别的候选基因呈现出动态表达模式，其表达变化始终先于形态分化的出现，且被推测参与调控塑性表型的起始过程。在各功能类别内部，我们观察到显著的共表达现象；同时通过转录因子结合位点（transcription factor binding site）分析，探究了这些基因共调控的潜在基础。我们提出了慈鲷LPJ可塑性的调控网络模型，并提供了骨骼与肌肉组织间存在调控串扰的证据，该串扰被推测可促进这一高度整合性状的发育。本研究将发育时间序列纳入表型可塑性研究，最终鉴定出一个相互关联、可响应环境信号的调控网络，该网络塑造了东非慈鲷这一关键创新性状的可塑性发育过程。