Wang Fang, Tekle Yonas I
Department of Biology, Spelman College, Atlanta, GA, United States.
Front Ecol Evol. 2022;10. doi: 10.3389/fevo.2022.851816. Epub 2022 Aug 4.
The evolution and diversity of the supergroup Amoebozoa is complex and poorly understood. The supergroup encompasses predominantly amoeboid lineages characterized by extreme diversity in phenotype, behavior and genetics. The study of natural selection, a driving force of diversification, within and among species of Amoebozoa will play a crucial role in understanding the evolution of the supergroup. In this study, we searched for traces of natural selection based on a set of highly conserved protein-coding genes in a phylogenetic framework from a broad sampling of amoebozoans. Using these genes, we estimated substitution rates and inferred patterns of selective pressure in lineages and sites with various models. We also examined the effect of selective pressure on codon usage bias and potential correlations with observed biological traits and habitat. Results showed large heterogeneity of selection across lineages of Amoebozoa, indicating potential species-specific optimization of adaptation to their diverse ecological environment. Overall, lineages in Tubulinea had undergone stronger purifying selection with higher average substitution rates compared to Discosea and Evosea. Evidence of adaptive evolution was observed in some representative lineages and in a gene (Rpl7a) within Evosea, suggesting potential innovation and beneficial mutations in these lineages. Our results revealed that members of the fast-evolving lineages, and Cutosea, all underwent strong purifying selection but had distinct patterns of codon usage bias. For the first time, this study revealed an overall pattern of natural selection across the phylogeny of Amoebozoa and provided significant implications on their distinctive evolutionary processes.
变形虫超群的进化与多样性十分复杂，目前了解甚少。该超群主要包含变形虫类谱系，其在表型、行为和遗传学方面具有极高的多样性。对变形虫超群物种内部和之间作为多样化驱动力的自然选择进行研究，将对理解该超群的进化起到关键作用。在本研究中，我们基于一组高度保守的蛋白质编码基因，在一个系统发育框架内，从广泛采样的变形虫中寻找自然选择的痕迹。利用这些基因，我们用各种模型估计了替换率，并推断了谱系和位点上的选择压力模式。我们还研究了选择压力对密码子使用偏好的影响，以及与观察到的生物学特征和栖息地的潜在相关性。结果表明，变形虫超群各谱系的选择存在很大异质性，这表明可能存在物种特异性的优化，以适应其多样的生态环境。总体而言，与盘状亚门和扁裸藻亚门相比，管足亚门的谱系经历了更强的纯化选择，平均替换率更高。在一些代表性谱系以及扁裸藻亚门中的一个基因（Rpl7a）中观察到了适应性进化的证据，这表明这些谱系中可能存在潜在的创新和有益突变。我们的结果表明，快速进化谱系的成员以及裸变亚门都经历了强烈的纯化选择，但具有不同的密码子使用偏好模式。本研究首次揭示了变形虫超群系统发育中的自然选择总体模式，并对其独特的进化过程提供了重要启示。
