Phenotypic variation among species is a product of evolutionary changes to developmental programs^1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium—an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.

物种间的表型变异是发育程序进化变化的产物^1,2。然而，这些变化如何产生新的形态特征仍不清楚。在这里，我们研究了哺乳动物滑膜或滑膜的基因组和发育基础，这是一种在不同谱系中反复进化的适应性特征，包括密切相关的有袋动物物种。通过对来自滑翔物种和非滑翔物种的 15 个有袋动物基因组进行比较基因组分析，我们发现Emx2基因座在滑翔物种中经历了谱系特异性的加速顺式调控进化模式。通过结合表观基因组学、转录组学和袋内有袋动物转基因技术，我们证明Emx2是有袋动物发育的关键上游调节因子。此外，我们还确定了不同的顺式调控元件，这些元件可能导致滑翔物种中Emx2表达水平增加。最后，通过小鼠功能实验，我们发现了滑翔机中Emx2表达模式可能是根据所有哺乳动物中预先存在的程序进行修改的证据。总之，我们的结果表明，patagia 反复起源于基因组趋同进化过程，其中Emx2的调节被独立进化物种中不同的顺式调节元件所改变。因此，针对同一关键发育基因的不同调控元件可能构成一种有效的策略，通过该策略，自然选择利用有袋动物基因组中的调控进化来产生表型新颖性。