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Ad Astra-funded PhD studentship Opportunity

SBES Ad Astra-funded PhD studentship Opportunity

Title: Deciphering the evolution and fine-tuning of vertebrate chemosensory systems using comparative genomics

About the project

Animal adaptation to different environments involves the accumulation of changes in physiology, feeding ecology, social structures, environmental habitats and circadian rhythm. As such, the ability to infer and process environmental chemosensory information is a crucial step in adopting a novel niche, placing sensory perception at the forefront of evolutionary adaptation.

Sensory perception is governed by a variety of different ‘sense-specific’ membrane-bound 7-transmembrane G-protein coupled receptor gene families encoded throughout the genome, e.g. olfactory receptors, trace amine-associated receptors, vomeronasal receptors and taste receptors. Each gene family contains varying numbers of coding sequences expressed in numerous cell types on different sense organs. The fine-tuning of these different sensory modes reflect life-history traits (e.g. sociality), niche-specific evolutionary adaptations (e.g. diet) and available sensory-space. However the relationships between these remain poorly understood.  

Given the current trend of cheaper sequencing costs, there are now more vertebrate genomes available than ever before, allowing an unprecedented, in-depth exploration of sensory evolution at the genomics level in a taxonomically diverse sample set. This project will combine comparative genomics, bioinformatics and phylogenetics to explore chemosensory evolution, answering questions such as ‘what is the background rate of evolution in chemosensory genes?’, ‘Do convergent life-history traits reflect sensory sequence convergence?’, ‘Does positive selection at key residues reflect lineage-specific spectral tuning?’, ‘When is loss of sensory function adaptive?’  

Core objectives in this project that you will research include:

Objective 1: Establishing rates of evolution, loss of function and duplication across sensory genes and background rates of gene evolution

Objective 2: Develop novel methods to explore positive selection in multigene families.

Objective 3: Correlate loss, gain and lineage-specific sensory evolution with life-history traits and ecological niche adaptation to explore available sensory-spaces, e.g. diet, sociality and pheromones and odorants.

Objective 4: Reconstruct ancestral sensory gene repertoires across the species tree, comparing extant and ancestral gene evolution over vast time-frames.

This project is an Ad Astra-funded studentship, and will be largely completed in silico, using the latest computational methods. Informal enquiries are welcome. The studentships are open to EU and non-EU candidates and are for a maximum of four years, renewable each year, subject to satisfactory progress. UCD supports equal opportunities and does not discriminate against individuals on the basis of gender, age, race, colour, nationality, ethnic or national origin, religion, marital status, family status, sexual orientation, disability or membership of the traveller community.

Requirements

  • Applicants must have, or expect to have, reached a minimum of an upper second-class (2.1) degree or equivalent in a relevant honours Bachelor’s or Master’s degree in a relevant biological/computational/mathematical field.
  • Excellent written and oral communication skills and a high level of competence in the English language are essential.
  • Experience working with quantitative and qualitative data

Desirable

  • Due to the computational nature of this project, applicants are expected to be familiar with a Linux OS, and command line usage.
  • A programming language, e.g. Python or Perl is desirable, though not necessary. It is expected that the applicant will learn and become proficient in at least one of these languages throughout the project.
  • Experience using R.
  • An MSc in a related field

Application Details

Applicants should submit the following g.hughes@ucd.ie as a single .pdf document:

1. A cover letter outlining their interest in the project and any relevant experience
2. A detailed CV
3. The names and contact details of two academic referees

Interviews will take place via video call in early August, and the PhD will be expected to commence in September 2020.

Funding Notes

The studentship award includes full tuition fee waiver, a PhD stipend of €18,000 per annum, and a research budget to cover research costs associated with the project.

Further info

For further information and to apply, please contact Dr. Graham Hughes

Email: g.hughes@ucd.ie

https://people.ucd.ie/g.hughes

Closing date

28th July 2020