Data from: Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming's lucky fungus

Eighty years ago, Alexander Fleming described the antibiotic effects of a fungus that had contaminated his bacterial culture, kick starting the antimicrobial revolution. The fungus was later ascribed to a putatively globally distributed asexual species, Penicillium chrysogenum. Recently, the species has been shown to be genetically diverse, and possess mating-type genes. Here, phylogenetic and population genetic analyses show that this apparently ubiquitous fungus is actually composed of at least two genetically distinct species with only slight differences detected in physiology. We found each species in air and dust samples collected in and around St Mary’s Hospital where Fleming worked. Genotyping of 30 markers across the genome showed that preserved fungal material from Fleming’s laboratory was nearly identical to derived strains currently in culture collections and in the same distinct species as a wild progenitor strain of current penicillin producing industrial strains rather than the type species P. chrysogenum. Global samples of the two most common species were found to possess mating-type genes in a near 1:1 ratio, and show evidence of recombination with little geographic population subdivision evident. However, no hybridization was detected between the species despite an estimated time of divergence of less than 1 MYA. Growth studies showed significant interspecific inhibition by P. chrysogenum of the other common species, suggesting that competition may facilitate species maintenance despite globally overlapping distributions. Results highlight under-recognized diversity even among the best-known fungal groups and the potential for speciation despite overlapping distribution.八十余年前，亚历山大·弗莱明（Alexander Fleming）报道了一株污染其细菌培养物的真菌所产生的抗菌活性，由此拉开了抗菌革命的序幕。该真菌后续被归为一种推测为全球分布的无性物种——产黄青霉（Penicillium chrysogenum）。近期研究证实，该物种不仅遗传多样性丰富，且携带有交配型基因。本研究通过系统发育与群体遗传分析发现，这一外观上遍布各处的真菌实则至少包含两个遗传层面截然不同的物种，二者在生理特征上仅存在细微差异。我们在弗莱明曾工作过的圣玛丽医院（St Mary’s Hospital）内外采集的空气与尘埃样本中，均分离到了这两个物种。对全基因组30个遗传标记位点的基因分型结果显示，弗莱明实验室保存的真菌菌株与当前保藏于各菌种保藏机构的衍生菌株几乎完全一致；且该菌株与当前工业产青霉素菌株的野生祖先菌株同属一个独特物种，而非模式种产黄青霉（Penicillium chrysogenum）。对全球范围内采集的两个最常见物种样本的分析显示，二者携带的交配型基因比例接近1:1，且存在重组迹象，群体在地理上几乎无明显分化。不过，尽管二者的估计分化时间不足1百万年，却未检测到物种间的杂交现象。生长实验结果显示，产黄青霉（Penicillium chrysogenum）对另一常见物种存在显著的种间抑制作用，这表明即便二者的全球分布范围存在重叠，种间竞争或可维持两个物种的独立性。本研究结果凸显出，即便是最广为人知的真菌类群，其内部也存在未被充分认知的物种多样性；同时也证实，即便分布范围重叠，物种形成过程仍有可能发生。