Table1_EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification.docx

Vision is among the oldest and arguably most important sensory modalities for animals to interact with their external environment. Although many different eye types exist within the animal kingdom, mounting evidence indicates that the genetic networks required for visual system formation and function are relatively well conserved between species. This raises the question as to how common developmental programs are modified in functionally different eye types. Here, we approached this issue through EyeVolve, an open-source PYTHON-based model that recapitulates eye development based on developmental principles originally identified in Drosophila melanogaster. Proof-of-principle experiments showed that this program’s animated timeline successfully simulates early eye tissue expansion, neurogenesis, and pigment cell formation, sequentially transitioning from a disorganized pool of progenitor cells to a highly organized lattice of photoreceptor clusters wrapped with support cells. Further, tweaking just five parameters (precursor pool size, founder cell distance and placement from edge, photoreceptor subtype number, and cell death decisions) predicted a multitude of visual system layouts, reminiscent of the varied eye types found in larval and adult arthropods. This suggests that there are universal underlying mechanisms that can explain much of the existing arthropod eye diversity. Thus, EyeVolve sheds light on common principles of eye development and provides a new computational system for generating specific testable predictions about how development gives rise to diverse visual systems from a commonly specified neuroepithelial ground plan.

视觉是动物与外界环境互动时最古老，也堪称最为重要的感官模态之一。尽管动物界存在着多种多样的眼型，但越来越多的研究证据表明，支撑视觉系统形成与功能发挥的遗传网络在不同物种间相对保守。这便引出了一个核心问题：在功能各异的眼型中，保守的发育程序是如何被修饰改造的？为此，我们借助开源的基于Python（PYTHON）开发的模型EyeVolve来解决这一问题——该模型基于最初在黑腹果蝇（Drosophila melanogaster）中发现的发育原理，复刻眼发育过程。原理验证实验表明，该程序的动态时序模型可成功模拟早期眼组织扩增、神经发生与色素细胞形成过程，实现从无序的祖细胞池，到由支持细胞包裹的高度有序的感光细胞簇晶格的连续转变。进一步而言，仅需微调五项参数——祖细胞池大小、奠基细胞与边缘的距离及位置、感光细胞亚型数量，以及细胞死亡决策——即可预测出大量不同的视觉系统构型，这与幼虫和成虫节肢动物中观察到的多样眼型高度相似。这提示存在普适性的底层机制，可解释节肢动物眼型多样性的绝大多数成因。综上，EyeVolve阐明了眼发育的共同原理，并为探究“发育如何从统一的神经上皮基底构型，产生多样化的视觉系统”提供了全新的计算框架，可生成具体的可验证预测。