National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America.
PLoS One. 2018 Apr 13;13(4):e0195571. doi: 10.1371/journal.pone.0195571. eCollection 2018.
The results of our recent study on mathematical modeling of microbial genome evolution indicate that, on average, genomes of bacteria and archaea evolve in the regime of mutation-selection balance defined by positive selection coefficients associated with gene acquisition that is counter-acted by the intrinsic deletion bias. This analysis was based on the strong assumption that parameters of genome evolution are universal across the diversity of bacteria and archaea, and yielded extremely low values of the selection coefficient. Here we further refine the modeling approach by taking into account evolutionary factors specific for individual groups of microbes using two independent fitting strategies, an ad hoc hard fitting scheme and a mixture model. The resulting estimate of the mean selection coefficient of s∼10-10 associated with the gain of one gene implies that, on average, acquisition of a gene is beneficial, and that microbial genomes typically evolve under a weak selection regime that might transition to strong selection in highly abundant organisms with large effective population sizes. The apparent selective pressure towards larger genomes is balanced by the deletion bias, which is estimated to be consistently greater than unity for all analyzed groups of microbes. The estimated values of s are more realistic than the lower values obtained previously, indicating that global and group-specific evolutionary factors synergistically affect microbial genome evolution that seems to be driven primarily by adaptation to existence in diverse niches.
我们最近关于微生物基因组进化数学建模的研究结果表明，平均而言，细菌和古菌的基因组在由与基因获得相关的正选择系数定义的突变-选择平衡状态下进化，这种进化被内在的删除偏差所抵消。这项分析基于一个强有力的假设，即基因组进化的参数在细菌和古菌的多样性中是普遍存在的，并且产生了极低的选择系数值。在这里，我们通过使用两种独立的拟合策略，即特定于微生物个别群体的进化因素，进一步细化了建模方法，即专门的硬拟合方案和混合模型。由此得出的与获得一个基因相关的平均选择系数 s∼10-10 的估计值表明，平均而言，获得一个基因是有益的，微生物基因组通常在弱选择状态下进化，这种状态可能会在具有大有效种群大小的高度丰富的生物中过渡到强选择。对更大基因组的明显选择压力被删除偏差所平衡，对于所有分析的微生物群体，删除偏差估计值都大于 1。估计的 s 值比以前获得的较低值更符合实际情况，这表明全局和群体特定的进化因素协同影响微生物基因组进化，这种进化似乎主要是由适应多样化生态位的驱动。
