Data from: Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum

Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus. IMPORTANCE: The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.

荚膜组织胞浆菌（Histoplasma capsulatum）是一类可引发致死性肺部感染的致病真菌。在美国，每年约有50万人暴露于荚膜组织胞浆菌，且超过60%的美国人口在人生的某个阶段曾接触过该真菌。我们对代表4个已确认的组织胞浆菌病地方流行区域的30株组织胞浆菌分离株开展了全基因组群体遗传学与系统发育分析，结果显示组织胞浆菌属（Histoplasma）至少包含4个遗传隔离且极少发生基因交流的物种。据此，我们提议对该属进行分类学重排。

研究意义：催生新型致病菌谱系的进化过程，对于我们理解致病菌如何适应新环境、以及不同菌株间基因交换的频率具有关键意义。真菌致病菌荚膜组织胞浆菌为精准验证新遗传变异起源的相关假说提供了理想的研究模型。我们的研究发现，荚膜组织胞浆菌复合体至少包含4个遗传特征与致病力均存在差异的隐存种。上述结果对组织胞浆菌病的流行病学研究具有重要参考价值，因为不同组织胞浆菌物种的地理分布范围与致病能力并不一致。