Archival mitogenomes identify invasionby the Batrachochytrium dendrobatidisCAPE lineage caused an African amphibianextinction in the wild

Abstract

Outbreaks of emerging infectious diseases are influenced by localbiotic and abiotic factors, with host declines occurring when conditionsfavour the pathogen. Deterioration in the population of the micro-endemic Tanzanian Kihansi spray toad (Nectophrynoides asperginis) occurredafter the construction of a hydropower dam, implicating habitatmodification in this species decline. Population recovery followed habitataugmentation; however, a subsequent outbreak of chytridiomycosis causedby Batrachochytrium dendrobatidis (Bd) led to the spray toad's extinction inthe wild. We show using spatiotemporal surveillance and mitogenomeassembly of Bd from archived toad mortalities that the outbreak wascaused by invasion of the BdCAPE lineage and not the panzootic lineageBdGPL. Molecular dating reveals an emergence of BdCAPE across southernAfrica overlapping with the timing of the spray toad's extinction. Thatour post-outbreak surveillance of co-occurring amphibian species in theUdzungwa Mountains shows widespread infection by BdCAPE yet nosigns of ill-health or decline suggests these other species can tolerateBd when environments are stable. We conclude that, despite transientsuccess in mitigating the impact caused by dams' construction, invasion byBdCAPE caused the ultimate die-off that led to the extinction of the Kihansispray toad