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.

适应辐射（adaptive radiation）的核心特征为同一演化支系内适应性分化与快速物种形成相互交织，最终产生大量生态特化、表型多样的物种。已有假说提出，适应辐射可起源于在适应性性状上具备显著表型可塑性（phenotypic plasticity）的祖先支系，该特性可推动由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在东非丽鱼科鱼类多个支系的摄食器官（trophic apparatus）基因表达模式中的体现形式，并验证观测到的表达模式是否支持遗传同化假说。本研究采用分窝实验设计（split brood experimental design），对比了处于适应辐射内外的物种的适应性可塑性水平。研究通过为个体投喂硬、软两种不同食物，诱导其压碎型咽颌（crushing pharyngeal jaws）产生可塑性响应。研究发现，非辐射起源的基干支系相较于衍生的辐射支系，展现出更高水平的适应性形态可塑性，这表明在适应辐射形成过程中，这些可塑性差异已发生了部分遗传固定。本研究还鉴定出两个可能经历了遗传同化的候选基因gif与alas1，同时观测到压碎型咽颌模式调控网络的连接模式发生改变。综合来看，本研究结果表明，在东非丽鱼的适应辐射过程中，遗传同化可能抑制了可塑性相关基因的诱导表达能力，使得反应规范（reaction norms）趋于平缓，并渠化了其摄食表型，最终推动物种向愈发狭窄的生态位（ecological niches）适应。