Understanding the relationship between ecological niche, coinfection and inter-lineage rate of recombination in a multihost pathogen

Theme: Evolution & Adaptation

Primary Supervisor:

Francois Balloux

Genetics, Evolution and Environment, UCL

Francois Balloux's Profile Picture

Secondary Supervisor:

Trent Garner

Evolution and Molecular Ecology Theme, IOZ

Trent Garner's Profile Picture

Additional Supervisor(s):
Matthew Fisher (Imperial College)

Project Description:

Batrachochytrium dendrobatidis (Bd) is responsible for the greatest loss of biodiversity attributable to infectious disease. Bd is geographically structured globally with only two places on earth harbouring multiple major lineages; one of which is in South Africa. Our field data indicate distinct but overlapping environmental envelopes for these two lineages, providing opportunities for lineage co-circulation, co-infection and recombination.

The student will first use state-of-the art long-read genome sequences (PacBio) and RNA-seq data to solve the genetic architecture of the main Bd lineages and reconstruct, for the first time, the extent of the Bd pan-genome (the set of accessory genes found only in a subset of strains). These best-in-class genomes will then be leveraged to understand the patterns of segregation that we see in Bd recombinants from South Africa.

Alongside genomics, the student will have the opportunity to generate drug-resistant mutants via laboratory passage to explore whether selectable markers can be generated allowing to determine whether Bd recombinants can be generated in vivo and in vitro. Then, working with our partners in South Africa, we will expand our current knowledge of Bd lineage distributional overlaps. Our partners are already monitoring ongoing patterns of climate change for a related project on impacts on Bd phenotypic trait variation, thus offering access to the key datasets required to explore climate-driven Bd lineage interactions at a fine scale.

Policy Impact of Research:

Changes in the distribution of Bd lineages caused by amphibian trade and/or climate change is likely to increase co-circulation of different lineages, leading to increased risk of emergence of novel recombinant Bd variants. This project will provide a comprehensive assessment of the likelihood and associated risks of this threat.

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