Supplementary Material for: Evolution of Patchily Distributed Proteins Shared between Eukaryotes and Prokaryotes: <i>Dictyostelium</i> as a Case Study

Protein families are often patchily distributed in the tree of life; they are present in distantly related organisms, but absent in more closely related lineages. This could either be the result of lateral gene transfer between ancestors of organisms that encode them, or losses in the lineages that lack them. Here a novel approach is developed to study the evolution of patchily distributed proteins shared between prokaryotes and eukaryotes. Proteins encoded in the genome of cellular slime mold <i>Dictyostelium discoideum</i> and a restricted number of other lineages, including at least one prokaryote, were identified. Analyses of the phylogenetic distribution of 49 such patchily distributed protein families showed conflicts with organismal phylogenies; 25 are shared with the distantly related amoeboflagellate <i>Naegleria</i> (Excavata), whereas only two are present in the more closely related <i>Entamoeba</i>. Most protein families show unexpected topologies in phylogenetic analyses; eukaryotes are polyphyletic in 85% of the trees. These observations suggest that gene transfers have been an important mechanism for the distribution of patchily distributed proteins across all domains of life. Further studies of this exchangeable gene fraction are needed for a better understanding of the origin and evolution of eukaryotic genes and the diversification process of eukaryotes.蛋白质家族在生命之树中的分布往往呈现斑块状格局：它们存在于亲缘关系较远的生物类群中，却在亲缘关系更近的支系中缺失。这种分布模式可能源于编码该蛋白的生物祖先之间发生的水平基因转移（lateral gene transfer），或是在缺失该蛋白的支系中发生了基因丢失事件。本研究开发了一种全新的研究方法，用以探究原核生物（prokaryotes）与真核生物（eukaryotes）之间共享的、斑块状分布的蛋白质家族的演化历程。研究团队鉴定出了在细胞黏菌盘基网柄菌（*Dictyostelium discoideum*）基因组中编码的蛋白质，以及包括至少一种原核生物在内的其他有限数目的支系中的同源蛋白。对49个此类斑块状分布蛋白质家族的系统发育分布进行分析后发现，其演化关系与物种系统发育树存在冲突：其中25个家族与亲缘关系较远的变形鞭毛虫纳格里属（*Naegleria*，古虫界Excavata）共享，而仅2个家族存在于亲缘关系更近的内阿米巴属（*Entamoeba*）中。大多数蛋白质家族的系统发育分析结果呈现出意料之外的拓扑结构：85%的系统发育树中，真核生物类群呈现多系起源的特征。上述观测结果表明，基因转移是推动斑块状分布蛋白质在所有生物域间传播的重要机制。为更深入理解真核生物基因的起源与演化，以及真核生物的多样化进程，还需对这类可转移基因组分开展进一步研究。