Gene family evolution of Caribbean coral

Gene family complexity and its influence of expression dynamics has long been theorized to be an important source of adaptation in natural systems through providing novel genetic material and influencing gene dosage. There is now growing empirical support for this theory; however, this process has only been demonstrated in a limited number of systems typically using recently diverged species or populations. In particular, examples of how this process operates in basal animals with deeper species splits has not been well explored. To address this issue, we investigated the evolution of gene family complexity in five species of common Caribbean coral. We demonstrate widespread divergence in gene repertoires owing to slow rates of gene turnover occurring along deep species splits. The resulting differences in gene family complexity involve numerous biologic processes, shedding light on to the selective forces that have influenced the evolution of each species. By coupling these findings with gene expression data, we show that increased gene family complexity promotes increased expression divergence between species, indicating an interplay between gene family complexity and expression divergence. Finally, we show that immune genes are evolving particularly fast demonstrating the importance of interactions with other organisms in the evolutionary history of Caribbean corals. Overall, these findings provide support for gene copy number change as an important evolutionary force in Caribbean corals, which may influence their ability to persist in a rapidly changing environment.

长期以来，学界普遍认为基因家族复杂度及其对基因表达动态的影响，是自然系统中适应性进化的重要来源——其通过提供新的遗传物质并调控基因剂量来发挥作用。目前，该理论的实证支持正日益增多，但相关演化过程仅在有限类群中得到验证，且研究对象多为新近分化的物种或种群，针对伴随深度物种分化事件的基干动物类群中该过程的运作模式，相关探索仍十分匮乏。为解决这一研究空白，本研究对5种常见加勒比海珊瑚的基因家族复杂度演化展开了系统性调查。结果显示，伴随深度物种分化事件发生的缓慢基因周转速率，广泛导致了各物种基因组成的分化，由此产生的基因家族复杂度差异涉及众多生物学过程，为解析塑造各物种演化轨迹的选择压力提供了新的研究视角。通过将上述发现与基因表达数据相结合，本研究证实基因家族复杂度的提升会显著促进物种间的表达分化，表明基因家族复杂度与表达分化之间存在相互作用。此外，本研究发现免疫基因的演化速率尤其迅速，这体现了生物间互作在加勒比海珊瑚演化历史中的重要性。总体而言，本研究结果支持基因拷贝数变异是加勒比海珊瑚演化的重要进化动力，该动力或可影响它们在快速变化的环境中存续的能力。