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 micro-endemic 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 toad's 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 toad's 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.

Diversification of spiny-throated reed frogs (Anura: Hyperoliidae) with the description of a new, range-restricted species from the Ukaguru Mountains, Tanzania.

The spiny-throated reed frog species group is a small radiation of Hyperolius frogs from East Africa. Unlike many members of the genus which have relatively wide distributions, these species tend to be small-range endemics found in montane and submontane forests. Recent discovery of a golden-hued frog with the clade-specific traits of spines on their gular discs prompted a morphological and genetic exploration of the distinctness of this new lineage and relationships to other members of the clade. Genetic (mitochondrial and nuclear loci) results resolved many sister-relationships, but deeper nodes in the phylogeny were poorly resolved. A reduced-representation genome-wide Single Nucleotide Polymorphism (SNP) dataset was able to fully resolve the phylogenetic relationships within this clade, placing this new lineage, here named after the mountain range in which is it found-H. ukaguruensis sp. nov., as an early diverging lineage within the group. This new species is distinct from all other spiny-throated reed frogs, necessitating further understanding as a single-mountain endemics vulnerable to habitat loss and potential decline. Morphometric analyses identify clear morphological characteristics that are distinct for the herein described species, most noticeably in that the eyes are significantly smaller than other members of the genus for which we have samples.