Department of Biology, Texas State University, San Marcos, TX, 78666, USA.
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
Nat Commun. 2024 Nov 28;15(1):10325. doi: 10.1038/s41467-024-53141-4.
Key innovations, traits that provide species access to novel niches, are thought to be a major generator of biodiversity. One commonly cited example of key innovation is pharyngognathy, a set of modifications to the pharyngeal jaws found in some highly species-rich fish clades such as cichlids and wrasses. Here, using comparative phylogenomics and phylogenetic comparative methods, we investigate the genomic basis of pharyngognathy and the impact of this innovation on diversification. Whole genomes resolve the relationships of fish clades with this innovation and their close relatives, but high levels of topological discordance suggest the innovation may have evolved fewer times than previously thought. Closer examination of the topology of noncoding elements accelerated in clades with the pharyngognathy innovation reveals hidden patterns of shared ancestry across putatively independent transitions to pharyngognathy. When our updated phylogenomic relationships are used alongside large-scale phylogenetic and ecological datasets, we find no evidence pharyngognathy consistently modifies the macroevolutionary landscape of trophic ecology nor does it increase diversification. Our results highlight the necessity of incorporating genomic information in studies of key innovation.
关键创新是物种进入新生态位的特征，被认为是生物多样性的主要来源之一。一个常见的关键创新的例子是咽颌，这是在一些高度物种丰富的鱼类进化枝中发现的咽颌的一系列修饰，如慈鲷和鲷鱼。在这里，我们使用比较系统基因组学和系统发育比较方法，研究了咽颌的基因组基础及其对多样化的影响。全基因组解决了具有这种创新的鱼类进化枝及其近亲的关系，但高水平的拓扑分歧表明，这种创新的进化次数可能比以前认为的要少。对具有咽颌创新的进化枝中非编码元件加速进化的拓扑结构的更仔细检查揭示了在假定独立的咽颌进化之间共享祖先的隐藏模式。当我们使用更新的系统基因组学关系以及大规模的系统发育和生态数据集时，我们没有发现咽颌一致地改变营养生态的宏观进化景观的证据，也没有增加多样化。我们的研究结果强调了在关键创新研究中纳入基因组信息的必要性。
