Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild

Outbreaks of emerging infectious diseases are influenced by local biotic
and abiotic factors, with host declines occurring when conditions favour
the pathogen. Deterioration in the population of the microendemic
Tanzanian Kihansi spray toad (Nectophrynoides asperginis) occurred after
the construction of a hydropower dam, implicating habitat modification in
this species decline. Population recovery followed habitat augmentation,
however a subsequent outbreak of chytridiomycosis caused
by Batrachochytrium dendrobatidis (Bd) led to the spray toads extinction
in the wild. We show using spatiotemporal surveillance and mitogenome
assembly of Bd from archived toad mortalities that the outbreak was caused
by invasion of the BdCAPE lineage and not the panzootic lineage BdGPL.
Molecular dating reveals an emergence of BdCAPE across Southern Africa
overlapping with the timing of the spray toads extinction. That our
post-outbreak surveillance of co-occurring amphibian species in the
Udzungwa Mountains shows widespread infection by BdCAPE yet no signs of
ill-health or decline suggests these other species can tolerate Bd when
environments are stable. We conclude that, despite transient success in
mitigating the impact caused by dams’ construction, invasion by BdCAPE
caused the ultimate die-off that led to the extinction of the Kihansi
spray toad.