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

Cite this dataset

Fisher, Matthew (2024). Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild [Dataset]. Dryad. https://doi.org/10.5061/dryad.nvx0k6f12

Abstract

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.

README: # 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/)

BEAST is required to open and analyse kihansi_cape_only_phylo.filtered.BIGBEAST.snps.vcf  (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

Methods

Datasets used in Kihansi Spray Toad analysis as described in Kihansi_ProcRSoc_ms_supptext

Funding

Natural Environment Research Council, Award: NE/S000844/1

MRC Centre, Award: MR/R015600/1