Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation.

Abstract

Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (<i>Batrachochytrium dendrobatidis</i> [<i>Bd</i>]). Prior research has revealed important insights into the biology and distribution of <i>Bd</i>; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of <i>Bd</i> that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of <i>Bd</i> samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of <i>Bd</i>, which we call <i>Bd</i>ASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (<i>Bd</i>GPL) in multiple localities. Additionally, we shed light on the global distribution of <i>Bd</i>GPL and highlight the expanded range of another lineage, <i>Bd</i>CAPE. Finally, we argue that more monitoring needs to take place where <i>Bd</i> lineages are coming into contact and where we know little about <i>Bd</i> lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history-and predict the future impacts-of this devastating pathogen.