CMPG, Institute of Ecology an Evolution, University of Berne, Baltzerstrasse 6, 3012, Berne, Switzerland.
Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
BMC Genomics. 2020 Mar 23;21(1):253. doi: 10.1186/s12864-020-6676-z.
Recent experimental work has shown that the evolutionary dynamics of bacteria expanding across space can differ dramatically from what we expect under well-mixed conditions. During spatial expansion, deleterious mutations can accumulate due to inefficient selection on the expansion front, potentially interfering with and modifying adaptive evolutionary processes.
We used whole genome sequencing to follow the genomic evolution of 10 mutator Escherichia coli lines during 39 days ( ~ 1650 generations) of a spatial expansion, which allowed us to gain a temporal perspective on the interaction of adaptive and non-adaptive evolutionary processes during range expansions. We used elastic net regression to infer the positive or negative effects of mutations on colony growth. The colony size, measured after three day of growth, decreased at the end of the experiment in all 10 lines, and mutations accumulated at a nearly constant rate over the whole experiment. We find evidence that beneficial mutations accumulate primarily at an early stage of the experiment, leading to a non-linear change of colony size over time. Indeed, the rate of colony size expansion remains almost constant at the beginning of the experiment and then decreases after ~ 12 days of evolution. We also find that beneficial mutations are enriched in genes encoding transport proteins, and genes coding for the membrane structure, whereas deleterious mutations show no enrichment for any biological process.
Our experiment shows that beneficial mutations target specific biological functions mostly involved in inter or extra membrane processes, whereas deleterious mutations are randomly distributed over the whole genome. It thus appears that the interaction between genetic drift and the availability or depletion of beneficial mutations determines the change in fitness of bacterial populations during range expansion.
最近的实验工作表明，在空间扩展过程中，细菌的进化动态可能与我们在充分混合条件下的预期有很大的不同。在空间扩展过程中，由于扩展前沿的选择效率低下，有害突变可能会累积，从而可能干扰和改变适应性进化过程。
我们使用全基因组测序来跟踪 10 个突变异形大肠杆菌（Escherichia coli）株在 39 天（约 1650 代）的空间扩展过程中的基因组进化，这使我们能够从时间角度了解适应和非适应进化过程在范围扩展过程中的相互作用。我们使用弹性网络回归来推断突变对菌落生长的积极或消极影响。在实验结束时，在所有 10 条线中，经过 3 天生长后测量的菌落大小均减小，并且突变在整个实验中以几乎恒定的速率积累。我们发现有证据表明有益突变主要在实验的早期积累，导致菌落大小随时间呈非线性变化。实际上，在实验开始时，菌落大小的扩展率几乎保持不变，然后在进化约 12 天后下降。我们还发现，有益突变在编码转运蛋白和膜结构的基因中富集，而有害突变在任何生物过程中都没有富集。
我们的实验表明，有益突变主要针对特定的生物功能，这些功能主要涉及跨膜或额外膜过程，而有害突变则随机分布在整个基因组中。因此，似乎遗传漂变和有益突变的可用性或耗尽之间的相互作用决定了细菌种群在范围扩展过程中适应度的变化。
