University of Leeds Featured PhD Programmes
Sheffield Hallam University Featured PhD Programmes
University College London Featured PhD Programmes
Norwich Research Park Featured PhD Programmes
University of Leeds Featured PhD Programmes

EASTBIO Phylogenomics on-the-fly: An automated evolutionary genomics pipeline for Drosophilidae

  • Full or part time
    Dr D Obbard
  • Application Deadline
    Sunday, January 05, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

Second Supervisor: Prof Michael Ritchie University of St Andrews

Drosophila melanogaster is one of the foremost genetic models, widely used in almost every area of experimental and comparative biology – from antiviral immunity to courtship behaviour. However, Drosophila’s unique value arguably lies in its suitability for comparative study: there are more than 3500 species in the family, and of these more than 300 of these can be readily cultured in the lab.

From the perspective of genome evolution, the Drosophila phylogeny has been valuable in answering questions of gene origin and evolution, the conservation of gene function, and the evolution of major chromosomal features such as telomeres and centromeres [e.g. 1,2]. From a comparative biology perspective, the Drosophila phylogeny has been used to answer fundamental questions about trait evolution at molecular, physiological, and behavioural levels [e.g. 3]

Surprisingly, although nearly 80 different Drosophila species have now been sequenced, there has not been a comprehensive study of genome evolution (or even a comprehensive genome-scale analysis of molecular evolution) since the first 20 or so were completed. This lost opportunity will only get worse as further genomes are sequenced (we estimate more than 50 more are in process or unpublished).

This project will construct a pipeline for analysis, and analyse, patterns of genome evolution across the Drosophilidae, aiming to incorporate between 70 and 100 species, as further sequencing becomes available. The precise focus of analyses, beyond phylogenetic inference, will depend on the student’s interests and aptitudes, but could include patterns of gene turnover, adaptive evolution, mutation patterns and rates, and phylogenetic mixed models linking genomic and phgenotypic traits. For a computationally focussed student, an ultimate aim of the project would be to automate these analyses and provide the pipeline to the wider research community.

High performance computing facilities are available, and depending on the students interests the project could include a practical component to sequence close outgroups.




Funding Notes

The “Visit Website” button will take you to our Online Application checklist. Complete each step and download the checklist which will provide a list of funding options and guide you through the application process. Follow the instructions on the EASTBIO website (you will be directed here from our application checklist), ensuring you upload an EASTBIO application form and transcripts to your application, and ticking the box to request references. Your referees should upload their references using the EASTBIO reference form, in time for the 5th January deadline so please give them plenty of time to do this by applying early.

References

[1] Drosophila 12 Genomes Consortium (2007) “Evolution of genes and genomes on the Drosophila phylogeny” Nature 450(7167) p203-18.

[2] Saint-Leandre et al (2019) “Diversification and collapse of a telomere elongation mechanism” Genome Research 10.1101/gr.245001.118

[3] Keesey et al (2019) “Inverse resource allocation between vision and olfaction across the genus Drosophila” Nature Communications 10:1162

Related Subjects

How good is research at University of Edinburgh in Biological Sciences?

FTE Category A staff submitted: 109.70

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

Email Now

Insert previous message below for editing? 
You haven’t included a message. Providing a specific message means universities will take your enquiry more seriously and helps them provide the information you need.
Why not add a message here
* required field
Send a copy to me for my own records.

Your enquiry has been emailed successfully





FindAPhD. Copyright 2005-2019
All rights reserved.