Whereas the gill chambers of jawless vertebrates open directly into the environment, jawed vertebrates evolved skeletal appendages that drive oxygenated water unidirectionally over the gills. A major anatomical difference between the two jawed vertebrate lineages is the presence of a single large gill cover in bony fishes versus separate covers for each gill chamber in cartilaginous fishes. Here, we find that these divergent patterns correlate with the pharyngeal arch expression of Pou3f3 orthologs. We identify a deeply conserved Pou3f3 arch enhancer present in humans through sharks but undetectable in jawless fish. Minor differences between the bony and cartilaginous fish enhancers account for their restricted versus pan-arch expression patterns. In zebrafish, mutation of Pou3f3 or the conserved enhancer disrupts gill cover formation, whereas ectopic pan-arch Pou3f3b expression generates ectopic skeletal elements resembling the multimeric covers of cartilaginous fishes. Emergence of this Pou3f3 arch enhancer >430 Mya and subsequent modifications may thus have contributed to the acquisition and diversification of gill covers and respiratory strategies during gnathostome evolution.

无颌脊椎动物的鳃室直接向环境开放，而有颌脊椎动物进化出骨骼附属物，可以单向驱动含氧水流过鳃。两种有颌脊椎动物谱系在解剖学上的一个主要区别是硬骨鱼有一个大的鳃盖，而软骨鱼的每个鳃腔都有单独的盖。在这里，我们发现这些不同的模式与 Pou3f3 直系同源物的咽弓表达相关。我们通过鲨鱼识别出一种存在于人类体内但在无颌鱼中检测不到的深度保守的 Pou3f3 拱形增强子。骨鱼和软骨鱼增强子之间的细微差别解释了它们的受限表达模式与泛弓表达模式。在斑马鱼中，Pou3f3 或保守增强子的突变破坏了鳃盖的形成，而异位泛拱 Pou3f3b 表达式生成异位骨骼元素，类似于软骨鱼类的多体覆盖物。这种 Pou3f3 弓增强子 > 430 Mya 的出现和随后的修改可能因此有助于在有颚动物进化过程中获得和多样化鳃盖和呼吸策略。