Evolutionary convergence provides natural opportunities to investigate how, when, and why novel traits evolve. Many convergent traits are complex, highlighting the importance of explicitly considering convergence at different levels of biological organization, or 'multi-level convergent evolution'. To investigate multi-level convergent evolution, we propose a holistic and hierarchical framework that emphasizes breaking down traits into several functional modules. We begin by identifying long-standing questions on the origins of complexity and the diverse evolutionary processes underlying phenotypic convergence to discuss how they can be addressed by examining convergent systems. We argue that bioluminescence, a complex trait that evolved dozens of times through either novel mechanisms or conserved toolkits, is particularly well suited for these studies. We present an updated estimate of at least 94 independent origins of bioluminescence across the tree of life, which we calculated by reviewing and summarizing all estimates of independent origins. Then, we use our framework to review the biology, chemistry, and evolution of bioluminescence, and for each biological level identify questions that arise from our systematic review. We focus on luminous organisms that use the shared luciferin substrates coelenterazine or vargulin to produce light because these organisms convergently evolved bioluminescent proteins that use the same luciferins to produce bioluminescence. Evolutionary convergence does not necessarily extend across biological levels, as exemplified by cases of conservation and disparity in biological functions, organs, cells, and molecules associated with bioluminescence systems. Investigating differences across bioluminescent organisms will address fundamental questions on predictability and contingency in convergent evolution. Lastly, we highlight unexplored areas of bioluminescence research and advances in sequencing and chemical techniques useful for developing bioluminescence as a model system for studying multi-level convergent evolution.

中文翻译：

---

复杂性状的多层次收敛与生物发光的演化

进化趋同为研究新特征如何、何时以及为何进化提供了自然的机会。许多趋同性状很复杂，突出了在生物组织的不同层次上明确考虑趋同或“多层次趋同进化”的重要性。为了研究多层次的趋同进化，我们提出了一个整体和分层的框架，强调将特征分解为几个功能模块。我们首先确定关于复杂性起源和表型收敛背后的不同进化过程的长期存在的问题，以讨论如何通过检查收敛系统来解决这些问题。我们认为生物发光是一种复杂的特性，通过新机制或保守的工具包进化了数十次，特别适合这些研究。我们提出了对整个生命之树至少 94 个独立生物发光起源的更新估计，我们通过审查和总结独立起源的所有估计来计算。然后，我们使用我们的框架来审查生物发光的生物学、化学和进化，并针对每个生物学级别确定我们系统审查中出现的问题。我们专注于使用共享荧光素底物腔肠素或 vargulin 产生光的发光生物，因为这些生物会聚进化出使用相同荧光素产生生物发光的生物发光蛋白。进化趋同不一定跨越生物水平，例如生物功能、器官、细胞、和与生物发光系统相关的分子。调查生物发光生物之间的差异将解决趋同进化中的可预测性和偶然性的基本问题。最后，我们重点介绍了生物发光研究的未探索领域以及测序和化学技术的进步，这些技术有助于将生物发光开发为研究多级趋同进化的模型系统。