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E4 DTP - African buffalo population genomics: understanding diversity and its drivers

  • Full or part time
    Dr L Morrison
  • Application Deadline
    Thursday, January 09, 2020
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Summary

Analyse genomic variation across African buffalo populations using a new reference genome and 239 whole genomes to understand African buffalo diversity and what influences that diversity.

Project background

The African buffalo (Syncerus caffer) is the most closely related African wild bovid to the domestic cow (Bos taurus). Selection pressure on buffalo populations is mostly environmentally derived (e.g. from pathogens). Buffalo are infected by all of the most important African cattle pathogens, but generally do not suffer the serious clinical disease seen in cattle; most likely due to prolonged co-evolution with pathogens selecting for disease control. The African buffalo therefore represents a uniquely valuable model in terms of understanding bovine coevolution with infectious disease, and how pathogens may have shaped buffalo populations.

This project benefits from a new high-quality de novo reference genome for S.caffer and a large collection of samples (n=239) whole-genome sequenced from across Africa including representatives of the four subspecies of S. caffer. This includes populations from areas that historically have been either endemic or free of specific pathogens or pathogen vectors. These data will enable the study of the impact of natural selection on the buffalo genome across evolutionary timescales.

Research questions

Q1. Which genetic variants are segregating within and between S. caffer sub-species?
Q2. What are the regions of S. caffer showing genomic adaptation, and the sites associated with potential co-adaptation to African pathogens (using comparative genomics, macroevolutionary analysis)?
Q3. Are there selective sweeps preferentially linked to different countries, areas and environments (microevolutionary analysis)?
Q4. What are the underlying genes and processes that underpin selection by pathogens in S. caffer?

Methodology

Year 1: The student will write a literature review and assay genetic polymorphisms across S. caffer subspecies and characterise the genetic landscape of S. caffer across Africa (Q1).
Year 2: The student will use the newly generated high-quality reference genome resource alongside genomes and polymorphism datasets from other bovidae to study selection at the macroevolutionary level (Q2), as well as compare polymorphism frequencies and patterns of linkage disequilibrium between S. caffer populations to detect selective sweeps linked to specific subpopulations and environments (Q3). A particular focus will be any evidence of selective sweeps linked to differences in pathogen exposure.
Year 3: Outputs from year 1 and 2 will be a first step towards both identifying underlying genes and processes that underpin the signatures of adaptation to pathogens in S. caffer (Q4).

Training

A comprehensive training programme will be provided comprising both specialist scientific training and generic transferable and professional skills.

Funding Notes

Requirements

Ideal candidates will have an upper second class degree in a related science, and have a background/interest in population genomics/genetics with a grounding in basic bioinformatics skills. An MSc in bioinformatics with knowledge of population genomics/genetics would be an advantage. The ability to learn programming skills to work with large-scale next-generation sequencing data (e.g. WGS, genomic variants, transcriptomics) is essential.

Application process - View Website

Apply by Thu Jan 09 2020 at 12:00

References

Meadows & Lindblad-Toh, 2017. Nature Reviews Genetics, 18, 624-636.
Zhang et al, 2014. Science, 346(6215): p. 1311-20.
Fennessy et al, 2016. Curr Biol, 26(18): p. 2543-9.

Related Subjects

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