PhD student in biology - Hiring in process/Finished, not possible to apply

Project description - Dynamics of genetic diversity within malaria infections

When studying outcomes of host-parasite interactions the genetic variation of the hosts is often taken into account. However, less consideration has been given the genetic variation of the pathogens that make up the infections and how this variation affects host-parasite interactions. When a host becomes infected by a pathogen, the infection seldom starts from a single pathogen “individual” but instead of a pathogen population that might consist of genetically different “individuals”. Once inside the host, different genetic variants of the pathogen can have different success. Some might be more successful at surviving and reproduce in the host whereas others might be fought of by the host's immune system or might not have the right genetic tools in order to invade the host cells. In this project we are focusing on the genetic variation that make up avian malaria infections. Avian malaria is related to the Plasmodium parasites that causes human malaria, but as a group they consist of more than thousands of different species that can infect birds both in temperate and tropical parts of the globe. When an infected mosquito takes a blood meal from the bird, the mosquito simultaneously injects a multitude of haploid malaria sporozoites into the avian host. As these sporozoites might be genetically different they might also have different success in multiplying and be retransmitted. With the use of different NGS-sequencing techniques we can now quantify and investigate the haplotype population of the parasites both between different infected hosts but also follow how the population changes over the course of a single infection. We are now seeking to employ a highly motivated bioinformatical orientated PhD student ideally with background in evolutionary biology. The aim of the project is to develop tools for quantifying haplotype diversity within and between infections and applying these methods to study 1) if and how the variation vary over the course of infections within and between host individuals 2) whether this variation is related to infection outcomes 3) the degree to which selection of haplotypes is acting between host species, both under experimental settings and in natural populations. Required QualificationsIn particular, the candidate should have:
1. A BSc or MSc in Bioinformatics or Biology (with documented skills in bioinformatics), ideally but not necessary with a background in evolutionary theory and ecology.
2. Practical skills in; a) UNIX/LINUX, b) handling of large data sets generated from NGS-sequencing, c) analyzing assembly and expression analysis of transcriptome data. d) variant calling
3. Some experience in molecular lab work.
4. A good understanding of statistics both practically and conceptually.
5. Excellent spoken and written English.
6. Willingness to conduct fieldwork

Eligibility

Basis of AssessmentMore specifically, we are looking for a highly motivated candidate with a strong scientific curiosity with the potential of conducting high quality scientific research. In line with this, candidate will be evaluated using the following criteria:1. The ability to work independently, formulate and solve scientific problems.2. The relevance and quality of qualifications, experience and publications and/or degree projects.3. The clarity of written and oral communication.4. The scientific quality and feasibility of the research plan (See below).
To facilitate assessment candidates are required to submit, together with their application, a motivational letter of why they want to do a PhD in ecology and evolution (1/2 page max), and a brief research plan outlining a project related to the background of this announcement, why this is important and how the ideas presented can be tested (max 1 page).
Students with basic eligibility for third-cycle studies are those who- have completed a second-cycle degree- have completed courses of at least 240 credits, of which at least 60 credits are from second-cycle courses, or- have acquired largely equivalent knowledge in some other way, in Sweden or abroad.

The employment of doctoral students is regulated in the Swedish Code of Statues 1998: 80. Only those who are or have been admitted to PhD-studies may be appointed to doctoral studentships. When an appointment to a doctoral studentship is made, the ability of the student to benefit from PhD-studies shall primarily be taken into account. In addition to devoting themselves to their studies, those appointed to doctoral studentships may be required to work with educational tasks, research and administration, in accordance with specific regulations in the ordinance.

Type of employment
Limit of tenure, four years according to HF 5 kap 7§.