Projects

 

Our current research projects are:

Leishmania population genomics
We aim for a global understanding of Leishmania populations. We focus on understanding fundamental aspects of population, quantitative and evolutionary genetics that will enhance our ability the control of the parasite. We currently have one PhD position and one postdoctoral position available. Get in touch if you are interested: daniel.jeffares@york.ac.uk.

Diversity landscape of  Leishmania infantum in Brazil
As part of the UK:Brazil Joint Centre Partnership in leishmaniasis we are using population genomics and quantitative genetic methods to understand the spread of Leishmania infantum in Brazil, and the effects of genetic diversity on disease severity and treatment outcomes.
Funders: Wellcome Trust, GCRF, MRC and FAPESP.
Collaborators: Jeremy Mottram (York), Carlos Henrique Nery Costa (Brazil), Elisa Cupolillo (Brazil)

Population genomics of  Leishmania donovani in Africa
Recent MRC funding will describe the diversity of Leishmania donovani in Ethiopia, Uganda, Kenya and Sudan.
Funder: MRC
Collaborators: Paul Kaye (York), Asrat Hailu (Ethiopia), Joseph Olobo (Uganda), Ahmed Musa (Sudan),  
Margaret Mbuchi (Kenya), Jane Mbui (Kenya).

» Genomics of the extremophile red alga Galdieria sulphuraria
With Seth Davies, we are investigating the weird and wonderful genome of Galdieria sulphuraria.
Funder: BBSRC

» Population genomics of plant pathogen Ralstonia solanacearum
With Ville Friman, we are applying population genomics to understand how R. solanacearum spreads through waterways in the UK and causes brown rot in potatoes.
Funder: BBSRC and NERC.

» 
Fission yeast population and functional genomics
I’ve used transposon mutagenesis of fission yeast to produce a fitness landscape of the fission yeast genome (see bioRxiv) and been involved in the analysis of of admixture with Jochen Wolf, see bioRxiv.

 

Transposon mutagenesis of fission yeast
Saturating mutagenesis of the fission yeast genome with the Hermes transposon allowed us to describe which regions were required for function, as a nucleotide-level resolution.

In the Bähler lab I described the genomic diversity of all known wild strains  conducting the first 220 genome-wide association studies (GWAS) for this species (Nature Genetics), examined the role of structural variation in the genome (Nature Communications), and the ability of fission yeast to make wine (PLOS One).
Funder: Wellcome Trust (to Jürg Bähler)

 

gwas3.
GWAS is feasible with microbes. Sequencing ~60 strains of fission yeast, and measuring dozens of traits allowed us to conduct genome wide association studies (GWAS), detecting hundreds of genetic variants that affect traits. This shows that GWAS is feasible for microbes, even with small very small sample sizes.

Daniel Jeffares has also studied:

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