Deploying bioinformatic and molecular ecology approaches to determine the diversity and significance of arthropod parasites and partners

Description

The ACCE DTP is committed to recruiting extraordinary future scientists regardless of age, disability, ethnicity, gender, gender identity, sexual orientation, faith or religious belief, pregnancy or maternity, parental or caring responsibilities or career pathway to date. We understand that a student’s potential can be shown in many ways and we strive to recruit students from all backgrounds, and support them on their scientific journey.

We have designed our application systems to identify candidates who are likely to be successful in research regardless of what opportunities may have been available to them prior to their application.

Various support and guidance on applying for an ACCE DTP studentship, including how to apply; what we’re looking for (including our assessment rubric); details of financial support, training, and placement opportunities available; and details of our recruitment process, can be found at https://accedtp.ac.uk, in the ‘prospective applicants’ tab.

Project overview

Background:

Arthropods are commonly subject to parasitism, are infected with pathogens, and may benefit from association with beneficial symbionts. These all live within the body of an individual. Traditional approaches to identification of parasites and partners utilized either visual scoring of parasite presence (along with dissection where necessary), or PCR screens of individuals for targets of interest. More recently, high throughput sequencing has enabled a new way of revealing associations as 'bycatch' in arthropod sequencing projects: when a target individual is removed from the field and DNA template purified, the sequence reflects both the target species and any other organisms (‘cobionts’) living within it. This project will exploit this secondary data to reveal the diversity and biology of the cobionts of arthropods.

Objectives:

1. Categorise cobiont parasites, pathogens and symbionts in sequencing reads from publicly available sequencing deposits derived from arthropods.

2. To develop genomic data for cobionts from under-represented groups, such as arthropod-infecting trypanosomes, microsporidia and nematodes, and use these data in a comparative genomic context to reveal patterns of evolution and diversification.

3. To establish novel interactions not previously known in the literature, and from these select particular cases for onward study of spatio-temporal dynamics and impact.

Novelty:

The use of secondary data from sequencing projects in ecology and evolution is transforming our capacity to understand the ecology and evolution of parasites and symbionts. Progress to date has largely focussed on bacterial symbionts. A key element of this project is to extend this approach to examine viruses, microeukaryotes and understudied groups such as entomopathogenic nematodes.

Skills and Training:

You will need to show evidence of an aptitude and enjoyment of bioinformatic analysis, but will be trained in the detection of parasites/symbionts in genomic data, genome assembly and analysis. We will also train the candidate in wet lab molecular ecology skills associated with detection of symbionts and parasites.

Essential and desirable criteria

Essential

• Zoology - particularly biological interrelationships (parasitism, symbiosis) and biological diversity of parasites and symbionts
• Molecular phylogenetics - how DNA sequence is used to estimate the relatedness of biological entities.
• Genetics/Genomics - an understanding of the construction of draft genomes from read data and comparative genomic analyses, and an aptitude for bioinformatics.

Desirable

• Field sampling techniques
• Knowledge of Molecular parasitology or molecular virology.

How to apply

Notes and details of how to apply are available here: https://accedtp.ac.uk/phd-opportunities/

All applicants to ACCE must complete the ACCE personal statement proforma. This is instead of a personal/supporting statement or cover letter. The proforma is designed to standardise this part of the application to minimise the difference between those who are given support and those who are not. Candidates should also submit a CV and the contact details of 2 referees.

Part-time study options

All ACCE PhDs are available as part time or full time, with part time being a minimum of 50% of full time. Please discuss potential part time arrangements with the primary supervisor before applying to the programme.

Project CASE status

This project is not a CASE project. While individual applicant quality is our overriding criterion for selection, the ACCE DTP has a commitment for 40% of all studentships to be CASE funded - as such, CASE projects may be favoured in shortlisting applicants when candidates are otherwise deemed to be equal or a consensus on student quality cannot be reached. This will only be done as a last resort for separating candidates.