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The amphibian‐infecting chytrid fungus, Batrachochytrium dendrobatidis (Bd), is widespread throughout Africa and is linked to declines of populations and species across the continent. While it is well established that the lineage of Bd encodes traits which determine disease severity, knowledge around how lineages are distributed according to environmental envelope is unclear. We here studied the distribution of Bd in South Africa based on the two lineages found, BdGPL and BdCAPE, in terms of their genome and environmental envelope statistically associated with their distribution. We used Bd surveillance data from published studies, as well as data collected during fieldwork from across South Africa, Lesotho, and eSwatini with samples collected along a transect spanning most of South Africa from Lesotho to the west coast. We utilized lineage‐typing qPCR to resolve the spatial distribution of BdGPL and BdCAPE across South Africa and used the resulting surveillance data to create a predictive ecological niche model for Bd lineages in South Africa. Phylogenomic analyses were performed on isolates sourced from across the transect. We show that BdGPL demonstrates a strong isolation by distance suggestive of stepping‐stone dispersal, while BdCAPE showed two distinct clusters within their genomic structure that appear geographically and temporally clustered, indicating two separate invasions. Our predictive niche model revealed that the two lineages tended to occur in different ecotypes; BdGPL was associated with lower altitude, arid regions while BdCAPE occurred across cooler, higher altitude environs. Niche predictions identified a zone of lineage contact, where genomics identified inter‐lineage recombinants. We argue that this zone of recombination should be prioritized for disease surveillance as it is a potential hotspot for the evolution of variants of amphibian chytrid with novel traits that may be epidemiologically relevant. The amphibian chytrid fungus has been seen to be widespread around the globe and consist of different genetic lineages. This fungus has recently been found to be able to form recombinant lineages between these existing genetic lineages, with still unknown consequences for the amphibian host. In South Africa, it was found that the hypervirulent global lineage has a wide environmental envelope creating the possibility for a number of contact zones where interlineage genetic recombination can occur, leading to recombinant lineages and potential new threats to the amphibian hosts.

Species in the fungal genus Batrachochytrium are responsible for severe declines in the populations of amphibians globally. The sources of these pathogens have been uncertain. O'Hanlon et al. used genomics on a panel of more than 200 isolates to trace the source of the frog pathogen B. dendrobatidis to a hyperdiverse hotspot in the Korean peninsula (see the Perspective by Lips). Over the past century, the trade in amphibian species has accelerated, and now all lineages of B. dendrobatidis occur in traded amphibians; the fungus has become ubiquitous and is diversifying rapidly. Science , this issue p. 621 ; see also p. 604 The chytrid fungus responsible for global amphibian declines originated in the Korean peninsula and spread during the past century by human trade. Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis , a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, Bd ASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.

1. According to the threat-sensitivity hypothesis, prey avoidance behaviour should reflect the magnitude of predation risk. Since predation can strongly affect reproduction success, ovipositing females are expected to adaptively adjust their predator avoidance response, or local breeding patch selectivity, in accordance with the perceived level of threat posed for their progeny by specific predators. However, association between avoidance and predation can be disrupted when the prey and the predator lack spatiotemporal opportunities to co-evolve, such as in cases of non-native predator introductions. 2. We examined the interactions between mosquitoes (from the genus Culex) and three species of sympatric predaceous freshwater fish, a native cyprinid Barbus paludinosus, & cichlid Pseudocrenilabrus philander and an introduced poeciliid, the western mosquitofish Gambusia affinis. 3. In an outdoor mesocosm experiment, we quantified patterns of Culex oviposition site selection across fish species using free-roaming, caged and fish-free treatments. In a complementary laboratory experiment, we tested the effectiveness of each fish species as predators of mosquito eggs and larvae. 4. Synthesis and applications. We found evidence for: (i) mosquito egg raft predation by freeroaming fish; (ii) fish-specific avoidance by ovipositing Culex; and (iii) a positive association between fish-specific oviposition avoidance and fish-specific efficiency as an egg predator. These results contribute towards a better understanding of predator-prey co-evolution, predator-borne cue recognition, and suggest local native fish, the southern mouthbrooder Pseudocrenilabrus philander, as an alternative to Gambusia for the biocontrol of Culex mosquitoes.

Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE ; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species ( Batrachochytrium dendrobatidis ) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.

Invasive and highly virulent parasites are emerging worldwide, transported to new locations and into novel hosts by anthropogenic activities. Multiple introduction events lead to interactions amongst genetically dissimilar genotypes that can result in either competitive exclusion, coexistence, or cycling through a combination of the two. Here, we report how intra-lineage trait variation of the multihost amphibian parasite Batrachochytrium dendrobatidis drives contrasting outcomes of inter-lineage interactions on two continents, Europe and Africa. Through field surveys, competition experiments and mathematical modelling we show that interactions between the same two lineages in the two continents and in different hosts demonstrate both ends of the exclusion/coexistence continuum. Trait variation in one of the two predominating lineages, BdGPL, is responsible for these contrasting outcomes: In Europe, BdGPL is highly competitive and has constrained the distribution of the other, BdCAPE, to two locations. In Africa, BdGPL and BdCAPE can mutually invade host populations when the other lineage is already resident, potentially leading to coinfections and recombination. That these contrasting outcomes are prolonged and contemporaneous for the same two lineages shows that epidemiological models of invasive parasites need to account for trait variation both within and across lineages.Competing Interest StatementThe authors have declared no competing interest.Footnotes* https://datadryad.org/stash/share/Lvro155J8hAqoESMBSm9Bdvd5eHCWDw6wEjEmzp2YX0

The ability to detect and monitor infectious disease in a phylogenetically informative manner is critical for their management. Phylogenetically informative diagnostic tests enable patterns of pathogen introduction or changes in the distribution of genotypes to be measured, enabling research into the ecology of the pathogen. Batrachochytrium dendrobatidis (Bd), a causative agent of chytridiomycosis in amphibian populations, emerged worldwide in the 21st century and is composed of six lineages which are display varying levels of virulence in their hosts. Research into the distribution, ecology and pathogenicity of these lineages has been hampered by an inability to type lineage efficiently. Here, we describe a lineage-specific TaqMan qPCR assay that differentiates the two lineages of Bd most commonly associated with chytridiomycosis: BdGPL and BdCAPE. We demonstrate how this assay can be used for the surveillance of wild populations of amphibians in Southern Africa using skin swabs, tissue samples and cultured isolates. Competing Interest Statement The authors have declared no competing interest.

Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into sterile culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to interested researchers worldwide as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been widely applied across at least 5 continents, 23 countries and in 62 amphibian species, and have been successfully used to isolate chytrids in remote field locations. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this important group of emerging fungal pathogens.