Data from: Long-term endemism of two highly divergent lineages of the amphibian-killing fungus in the Atlantic Forest of Brazil

The recent global spread of the amphibian-killing fungus [Batrachochytrium dendrobatidis (Bd)] has been closely tied to anthropogenic activities; however, regional patterns of spread are not completely understood. Using historical samples, we can test whether Bd was a spreading or endemic pathogen in a region within a particular time frame, because those two disease states provide different predictions for the regional demographic dynamics and population genetics of Bd. Testing historical patterns of pathogen prevalence and population genetics under these predictions is key to understanding the evolution and origin of Bd. Focusing on the Atlantic Forest (AF) of Brazil, we used qPCR assays to determine the presence or absence of Bd on 2799 preserved postmetamorphic anurans collected between 1894 and 2010 and used semi-nested PCRs to determine the frequency of rRNA ITS1 haplotypes from 52 samples. Our earliest date of detection was 1894. A mean prevalence of 23.9% over time and spatiotemporal patterns of Bd clusters indicate that Bd has been enzootic in the Brazilian AF with no evidence of regional spread within the last 116 years. ITS1 haplotypes confirm the long-term presence of two divergent strains of Bd (BdGPL and Bd-Brazil) and three spatiotemporally broad genetic demes within BdGPL, indicating that Bd was not introduced into southeast Brazil by the bullfrog trade. Our data show that the evolutionary history and pathogen dynamics of Bd in Brazil is better explained by the endemic pathogen hypothesis.近年来，致死两栖动物的真菌[蛙壶菌（Batrachochytrium dendrobatidis, Bd）]在全球范围内的扩散与人类活动紧密相关，但目前其区域传播模式尚未完全明晰。利用历史样本，我们可验证某一区域在特定时段内，蛙壶菌究竟属于外来扩散性病原体，还是当地固有的病原菌——这两种疾病状态会对该区域的病原体种群动态与群体遗传学特征给出截然不同的预测。基于此类预测验证病原体流行率与群体遗传学的历史模式，是阐明蛙壶菌演化与起源的关键所在。本研究聚焦巴西大西洋森林（Atlantic Forest, AF）区域，通过实时荧光定量聚合酶链反应（quantitative real-time polymerase chain reaction, qPCR）检测，对1894年至2010年间采集的2799份经固定保存的变态后无尾类标本开展蛙壶菌存在性检测；同时采用半巢式聚合酶链反应（semi-nested PCR）对52份样本的核糖体RNA ITS1单倍型频率进行分析。本次研究最早检出蛙壶菌的时间为1894年。研究时段内的平均流行率达23.9%，结合蛙壶菌聚类的时空分布模式，结果表明巴西大西洋森林内的蛙壶菌为当地长期定殖的固有病原菌，且过去116年间未出现区域性扩散。ITS1单倍型分析证实，该区域存在两种分化显著的蛙壶菌菌株（BdGPL与Bd-Brazil），且BdGPL支系内存在三个时空分布广泛的遗传类群，这说明蛙壶菌并非经由牛蛙贸易引入巴西东南部。本研究数据显示，巴西境内蛙壶菌的演化历史与病原体动态，更契合“固有病原菌假说”的解释。