Phylogenomics on-the-fly: An automated evolutionary genomics pipeline for Drosophilidae
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lost opportunity will only get worse as further genomes are sequenced (we estimate more than 50 more are in process or unpublished).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.
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If you would like us to consider you for one of our scholarships you must apply by 5 January 2020 at the latest.
 Drosophila 12 Genomes Consortium (2007) “Evolution of genes and genomes on the Drosophila phylogeny” Nature 450(7167) p203-18.
 Saint-Leandre et al (2019) “Diversification and collapse of a telomere elongation mechanism” Genome Research 10.1101/gr.245001.118
 Keesey et al (2019) “Inverse resource allocation between vision and olfaction across the genus Drosophila” Nature Communications 10:1162
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