DOI: 10.5061/dryad.nvx0k6f12
title: Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild

description: 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.
description: Datasets used in Kihansi Spray Toad analysis as described in
 Kihansi_ProcRSoc_ms_supptext
description: # # 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.xls**
 File type; geographical distance + Bd lineage assignment File type; xls
 Datatype; txt Usage notes: Open with Microsoft Excel variables;
 'Isolate' - Individual reference code 'Lat'; Latitude
 (decimal degrees) 'Long'; Longitude (decimal degrees)
 'Pop'; Population - GPL = global panzootic lineage genotypes;
 CAPE = CAPE lineage genotypes; KIHANSI - KIHANSI genotypes ## Usage notes
 **MEGA** is required to open and analyse
 *sequences_noInconsistentSites_04-01-21.fasta*
  ([https://www.megasoftware.net/](https://www.megasoftware.net/))
 **BEAST** is required to open and analyse
 *kihansi_cape_only_phylo.filtered.BIGBEAST.snps.vcf*
  ([https://beast.community/)](https://beast.community/) **Microsoft
 Excel** is required to open *geo_dist_kihansi_cape.xls
 *and *Pria_Tanzania_061119_lineagespecific_2.xls* ## Funding UK Natural
 environmental research council NERC