DataSheet_1_Continent-wide recent emergence of a global pathogen in African amphibians.docx

IntroductionEmerging infectious diseases are increasingly recognized as a global threat to wildlife. Pandemics in amphibians, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have resulted in biodiversity loss at a global scale. Genomic data suggest a complex evolutionary history of Bd lineages that vary in pathogenicity. Africa harbors a significant proportion of global amphibian biodiversity, and multiple Bd lineages are known to occur there; yet, despite the decline of many host species, there are currently no described Bd-epizootics. Here, we describe the historical and recent biogeographical spread of Bd and assess its risk to amphibians across the continent of Africa.
MethodsWe provide a 165-year view of host-pathogen interactions by (i) employing a Bd assay to test 4,623 specimens (collected 1908–2013); (ii) compiling 12,297 published Bd records (collected 1852–2017); (iii) comparing the frequency of Bd-infected amphibians through time by both country and region; (iv) genotyping Bd lineages; (v) histologically identifying evidence of chytridiomycosis, and (vi) using a habitat suitability model to assess future Bd risk.
ResultsWe found a pattern of Bd emergence beginning largely at the turn of the century. From 1852–1999, we found low Bd prevalence (3.2% overall) and limited geographic spread, but after 2000 we documented a sharp increase in prevalence (18.7% overall), wider geographic spread, and multiple Bd lineages that may be responsible for emergence in different regions. We found that Bd risk to amphibians was highest in much of eastern, central, and western Africa.
DiscussionOur study documents a largely overlooked yet significant increase in a fungal pathogen that could pose a threat to amphibians across an entire continent. We emphasize the need to bridge historical and contemporary datasets to better describe and predict host-pathogen dynamics over larger temporal scales.

引言
新发传染病正日益被视为对野生动物的全球性威胁。由真菌病原体蛙壶菌（Batrachochytrium dendrobatidis, Bd）引起的两栖动物流行病已在全球范围内造成生物多样性丧失。基因组学数据表明，Bd的不同谱系具有复杂的进化历史，且致病力存在差异。非洲拥有全球相当比例的两栖动物生物多样性，且已知当地存在多种Bd谱系；然而，尽管许多宿主物种数量下降，目前尚无关于Bd引发的动物流行病的报道。本研究阐述了Bd在非洲大陆的历史与近期生物地理传播情况，并评估了其对当地两栖动物的感染风险。

方法
本研究通过以下6项工作，构建了长达165年的宿主-病原体互作研究视角：(1) 利用Bd检测实验对1908年至2013年采集的4623份标本开展检测；(2) 整理1852年至2017年采集的12297条已发表的Bd相关记录；(3) 按国家和区域分别比较不同时期感染Bd的两栖动物的感染频率；(4) 对Bd谱系进行基因分型；(5) 通过组织学方法鉴定壶菌病（chytridiomycosis）的感染证据；(6) 利用生境适宜性模型评估未来Bd的感染风险。

结果
研究结果显示，Bd的传播主要始于20世纪之交。1852年至1999年期间，Bd的整体感染率较低（总体为3.2%），且地理传播范围有限；2000年之后，感染率大幅上升（总体达18.7%），地理传播范围扩大，同时多个Bd谱系可能是不同区域出现疫情的原因。本研究还发现，非洲东部、中部和西部大部分地区的两栖动物面临的Bd感染风险最高。

讨论
本研究证实，一种可对整个大陆的两栖动物构成威胁的真菌病原体出现了长期被忽视但却显著的传播增长。我们强调，有必要整合历史与当代数据集，以在更长的时间尺度上更好地描述和预测宿主-病原体的动态变化。