The spatial epidemiology and molecular evolution of panzootic amphibian chytridiomycosis

Modern-day amphibians are known to be suffering rates of extinction that far exceed any other class of vertebrates, including those experienced by mammals and birds, and nearly one third of amphibian species are threatened. The question of why amphibians are going extinct at these accelerated rates has puzzled scientists for three decades. A clue to the mystery came about when scientists working in Central America and Australia noted that the declines in amphibian biodiversity were spreading in a wave-like manner, from a point source. These patterns of decline were caused by an emerging infectious disease, and in 1997 researchers discovered the fungal pathogen and named it Batrachochytrium dendrobatidis (Bd).

Since then, our research has been focused on finding out where the fungus is, where it is spreading to and what its effect is on amphibian biodiversity. We have made a mapping tool at www.bd-maps.net and this has shown that Bd occurs on all continents with amphibians. However, not all species and populations infected with Bd die, suggesting to us that there may be more than one strain (or lineage) of Bd and that these are not all equally destructive. Confirmation of this came when we used new whole genome sequencing technology to sequence isolates of Bd from around the world. We discovered three lineages of Bd, and showed that only one of them is responsible for mass mortalities and species declines. We named this lineage BdGPL for 'Bd Global Panzootic Lineage' and showed that it occured in Africa, Europe, Australia and America.

Currently, several lines of argument suggest that BdGPL evolved in Africa. We will investigate this 'Bd Out-of-Africa' hypothesis by sequencing the genomes of Bd isolates widely across Africa and Europe, and undertaking fine-scale studies of the pathogens impact where it has been introduced into new environments. Our project will investigate both broad- and fine-scale processes, by characterising the genome diversity of Bd at the continental-level, but also focusing on fine-scale evolutionary patterns in Africa, the Pyrenees, the Alps and the UK. We will twin these genomic approaches with experimental approaches in order to determine whether invasive 'outbreak' lineages have altered their virulence and infectivity owing to accelerated evolution by the action of natural selection. Here, our expectation is that outbreak lineages that are adapting to new environments and hosts will have increased virulence and transmission rates when compared against the ancestral lineage in its original geographic background. These experiments will not only give us added certainty when determining the geographic origins of these infections, but will also allow us to assess why BdGPL is so much more virulent, and transmittable, than the other lineages of Bd.

More widely, our research will inform us about the risk that new pathogens pose to uninfected environments. Currently, we are seeing many emerging pathogenic fungi causing untold destruction to forests, bats and frogs. Perhaps there are common processes that underlie these emergences of disease - not only global trade in infected goods but also genome-level processes that are unique to fungi? Projects such as that described here hold the key to answering these important questions before losses of biodiversity increase further.

Direct academic/NGO/biotech users:

- We are collaborating with the Environmental Service group ADAS to develop a lateral-flow diagnostic assay for sensitive, specific and inexpensive PCR-independent detection of Bd. Knowledge of the diversity of global lineages of Bd is essential to correctly assay the specificity of this diagnostic technology and our NERC-funded data will feed into this, and other, diagnostic projects.

- Fisher and Garner sit on the UK Wildlife Health Committee with representatives from NGO's (Natural England) and the Government (DEFRA). The outputs from our research are reported to this committee via meetings on a bi-annual basis and provide a scientific basis for decisions on amphibian conservation in the UK

- Our results are fed directly to academics and NGO's in Iberia, Switzerland via the Project partners (Bosch and Schmidt) and our website www.bd-maps.eu. More widely, we will leverage our EU-wide research network BiodivERsA RACE (coordinated by Fisher) to disburse important discoveries as they occur. We collaborate widely with research groups in other continents and, as our project is global in its conception, we will undertake to disburse data on the spatial distribution of Bd lineages as it accrues, well in advance of publication, following our established practice. We are already exporting technical ability, including experimental approaches applicable to various nonmodel amphibian species, field methods for isolating pathogenic fungi and training in molecular diagnosis of infection. Labs and groups that have already benefited from our network number in the dozens and can be found on 3 continents. It is our every intention to continue to train researchers in the UK and abroad in the methods and analytical approaches we will use in this project.

Indirect users:

- Our population genomic data and the new methods that we are developing to handle, analyse and disburse it through the web are of broad interest to infectious disease epidemiologists as they represent the state-of-the-art tools for assessing the spread of new infection. We predict widespread impact here in terms of tools, data and high-impact publications.

Wider users:

- The general public understand the importance of emerging infections through their experience of recent epidemics/epizootics such as FMV, SARs & forest pathogens. We will continue to widely disseminate our findings via our effective use of the mass media, and we regularly interact with the global media including the BBC (World Service, Radio 4, Website), broadsheets (Guardian, Telegraph), National Public Radio (NPR: USA), the scientific press (New Scientist (x3), Science) and the French media using our wide range of media contacts and press offices. We will continue to work with NERC and have recently published an article with NERC 'Planet Earth' on the emergence of BdGPL and the associated role of the amphibian trade. We interact widely with schools via the Zoological Society of London and maintain a project specific blog at http://spatialepidemiology.blogspot.com/