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Genomic epidemiology of the emerging pathogen Batrachochytrium dendrobatidis from native and invasive amphibian species in Chile.
Valenzuela-Sánchez A
,
O'Hanlon SJ
,
Alvarado-Rybak M
,
Uribe-Rivera DE
,
Cunningham AA
,
Fisher MC
,
Soto-Azat C
.
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Emerging fungal diseases represent a threat to food security, animal and human health worldwide. Amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has been associated with catastrophic and well-documented amphibian population declines and extinctions. For the first time, Bd was cultured from native and non-native wild amphibians in Chile. Phylogenomic analyses revealed that Chilean isolates AVS2, AVS4 and AVS7 group within the global panzootic lineage of Bd (BdGPL) in a single highly supported clade that includes a genotype previously isolated from the United Kingdom. Our results extend the known distribution of BdGPL in South America and suggest a single and relatively recent introduction of BdGPL into the country, providing additional support to the role of anthropogenic activity in the global spread of this panzootic lineage.
Figure 1
(a) Sites of collection, amphibian species captured and Batrachochytrium dendrobatidis (Bd) [AVS4] isolate obtained from Chile. (b) Global phylogeny of 52 isolates of Bd based on 363,497 segregating sites. The clade containing the Chilean Bd isolates is highlighted in red, and the Chilean isolates are labelled in red: AVS4 from Xenopus laevis from Hualañé, AVS7 from Calyptocephalella gayi from Valdivia and AVS2 from Batrachyla antartandica from Melimoyu. The branches of the tree are weighted (thickness) by bootstrap support (500 replicates), with branches with 80% of support and above labelled [Colour figure can be viewed at wileyonlinelibrary.com]
Figure 2
A phylogenetic tree of Bd isolates with proportional branch lengths, based on a 1.66 Mb region of supercontig_1.2. This region includes a known loss of heterozygosity (LOH) event shared by all know BdGPL isolates. The Chilean isolates (labelled in red) form a clade (circled in red) with several isolates from Europe (0711.1, AoCH15, UKTvB and VA02) and one from Canada (JEL261). The branch labels indicate bootstrap support from 500 bootstrap replicates [Colour figure can be viewed at wileyonlinelibrary.com]
Figure 3
Sliding window analysis of population differentiation of Chilean Bd isolates against other BdGPL isolates using Weir and Cockerham's FST estimator. Each point represents a 10Kb genomic window, with a 5 kb step‐size. The dashed black line represents the mean FST (0.0679). The solid black line represents the 95% quantile threshold of the FST estimator (0.3141). Each point is sized and coloured on a log scale by the number of variants in each window. The legend indicates the colour scale (the number of SNPs included in each window varied from 1 to 177, with a median of 24). Point size from small to large is scaled from low to high numbers of variants [Colour figure can be viewed at wileyonlinelibrary.com]
