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 Mountai..., Datasets used in Kihansi Spray Toad analysis as described in Kihansi_ProcRSoc_ms_supptext, , # # Kihansi Spray Toad \"Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild\"

Main files associated with the manuscript

## Description of the data

**Pria_Tanzania_061119_lineagespecific_2.xls**

File type; quantitative PCR data\
File type; xls file\
Datatype; txt and numerical

variables;
'Well' - Individual well reference code range 1-96
'Well Position'; Individual well position range A1-G12
'Quencher'; Name of quencher dye 
'CT'; Cycle threshold. 'Undetermined' = no data. Otherwise numerical intensity value

**sequences_noInconsistentSites_04-01-21.fasta**

File type; MEGA readable FASTA file of Bd mtDNA
Datatype; csv file
File contains FASTA sequences of Bd mtDNA for import into MEGA

**kihansi_cape_only_phylo.filtered.BIGBEAST.snps.vcf**

File type; BEAST mtDNA vcf input file
Datatype; vcf
Usage notes: Open with any standard text editor
Vcf file for input into BEAST

**geo_dist_kihansi_cape.xl...