Data from: Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes

Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically-driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that non-radiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1 were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.

适应性辐射（Adaptive Radiation）的核心特征为同一演化支内伴随快速物种形成的适应性分化，最终产生诸多生态特化、表型多样的物种。已有研究提出，适应性辐射可起源于在适应性性状上具有显著表型可塑性（phenotypic plasticity）的祖先演化支，该过程会促进生态驱动的表型分化，并最终通过基因调控区域（gene regulatory regions）的遗传同化（genetic assimilation）得以固定。本研究旨在探究表型可塑性如何反映在东非慈鲷（East African cichlid fishes）多个演化支的摄食器官（trophic apparatus）基因表达模式中，并验证观测到的模式是否符合遗传同化假说。本研究采用分窝实验设计（split brood experimental design），对比适应性辐射内外物种的适应性可塑性水平。通过为实验个体投喂硬质或软质饵料，诱导其压碎型咽颌（crushing pharyngeal jaws）产生可塑性响应。研究结果显示，未发生辐射的基底演化支比衍生的辐射类群具有更高水平的适应性形态可塑性，这表明在适应性辐射形成过程中，此类差异已被部分遗传固定。研究同时鉴定出两个可能经历遗传同化的候选基因gif与alas1，并发现LPJ模式构建网络的调控通路发生了改变。综合来看，本研究结果表明，在东非慈鲷的适应性辐射过程中，遗传同化可能削弱了可塑性相关基因的诱导性，使得反应规范（reaction norms）趋于平缓，并使其摄食表型发生渠化，最终推动物种向日益狭窄的生态位适应。