Bacteriophages play key roles in microbial evolution^1,2, marine nutrient cycling³ and human disease⁴. Phages are genetically diverse, and their genome architectures are characteristically mosaic, driven by horizontal gene transfer with other phages and host genomes⁵. As a consequence, phage evolution is complex and their genomes are composed of genes with distinct and varied evolutionary histories^6,7. However, there are conflicting perspectives on the roles of mosaicism and the extent to which it generates a spectrum of genome diversity⁸ or genetically discrete populations^9,10. Here, we show that bacteriophages evolve within two general evolutionary modes that differ in the extent of horizontal gene transfer by an order of magnitude. Temperate phages distribute into high and low gene flux modes, whereas lytic phages share only the lower gene flux mode. The evolutionary modes are also a function of the bacterial host and different proportions of temperate and lytic phages are distributed in either mode depending on the host phylum. Groups of genetically related phages fall into either the high or low gene flux modes, suggesting there are genetic as well as ecological drivers of horizontal gene transfer rates. Consequently, genome mosaicism varies depending on the host, lifestyle and genetic constitution of phages.

中文翻译：

---

噬菌体的进化因宿主，生活方式和基因组而异。

噬菌体在微生物进化^1,2，海洋营养循环³和人类疾病^4中起关键作用。噬菌体在遗传上是多种多样的，它们的基因组结构具有特征性的镶嵌性，这是由与其他噬菌体和宿主基因组^5的水平基因转移驱动的。因此，噬菌体的进化是复杂的，其基因组由具有不同和不同的进化历史^6,7的基因组成。但是，关于镶嵌术的作用及其在多大程度上产生了基因组多样性谱⁸或遗传上不连续的种群^9,10，存在着相互矛盾的观点。。在这里，我们表明噬菌体在水平基因转移程度相差一个数量级的两个一般进化模式内进化。温带噬菌体分布于高和低基因通量模式，而裂解噬菌体仅共享较低基因通量模式。进化模式也是细菌宿主的函数，并且取决于宿主门，以任何一种模式分布不同比例的温带和裂解性噬菌体。几组与遗传相关的噬菌体属于高基因或低基因通量模式，表明水平基因转移速率既有遗传因素，也有生态因素。因此，基因组镶嵌术根据噬菌体的宿主，生活方式和遗传组成而变化。