PhD Scholarship Recombination rates in Seychelles warblers & long-tailed finches

Scholarship opportunities

We are looking for a student who wishes to design their own PhD research project researching recombination rates. You will be supervised by Hannah Dugdale (RUG; https://hannahdugdale.wordpress.com ), Susan Johnston (University of Edinburgh, https://sejohnston.com/ ), and Simon Griffith (MQ; https://griffithecology.com ). The work on the Seychelles warblers will be in collaboration with David S Richardson (University of East Anglia, UK; https://people.uea.ac.uk/david_richardson ) and on the long-tailed finches with Daniel Hooper (Columbia University, https://www.danielmarchooper.com/people ).

This is a double degree at RUG and MQ. For the first part of the PhD you will be based at RUG and embedded in the Seychelles Warbler Project (http://seychelles-warbler-project.group.shef.ac.uk ). You will conduct fieldwork in the Seychelles for a minimum of two seasons (up to 3 months per season), with a COVID-19 contingency plan. For the last two-years you will be based in Australia on the MQ campus. You will be part of a team of PhD students, post-docs, and staff who are using long-term individual-based datasets to improve understanding of life-history evolution.

As a PhD scholarship student, you will develop your own research project in consultation with the associated supervisors. You will conduct independent and original scientific research, report results via peer-reviewed publications, conference presentations, and ultimately a PhD thesis. The PhD thesis has to be completed within four years. Being part of a cutting-edge research programme, you will receive training in the form of hands-on instruction, advanced courses, summer/winter schools, as well as complementary workshops on generic research and transferable skills. Special attention is paid to training activities directed towards your future (academic or non-academic) career after the PhD trajectory, in the context of the RUG’s Career Perspective Series, and the Research Training Certification Program at MQ.

Project
Recombination is the crossing over of maternal with paternal chromosomes during reproduction. Recombination can generate and break-up both beneficial and detrimental genetic variation combinations in the resulting offspring. Novel genetic combinations may allow populations to respond to change, with fitness consequences, and can also be important in speciation. We have however a limited understanding of the causes and consequences of vartiation in recombination rates within and between individuals, and at speciation level. You will design your project to investigate these effects.

In The Netherlands, you will use the long-term Seychelles warbler dataset to address this question. Seychelles warblers are cooperative breeders and we have detailed life-history data of over 2,000 birds, spanning more than 30 years. We have whole genome sequencing data from 1,800 of these individuals at 5-15x coverage. Potential research questions are do recombination rates differ between individuals and are these differences heritable, and what are the fitness consequences of these differences.

In Australia, you will work on the recombination landscape of the Z chromosome in long-tailed finches, using a haplotagging dataset. Most of the Z chromosome appears to be a recombination desert in long-tailed finches but there are large inversions segregating.
Our inference about the process behind the supposed recombination desert on the long-tailed finch Z chromosome comes from high-linkage disequilibrium between subspecies and the low genetic diversity within subspecies within the interior of the Z chromosome. You will investigate the effect of inversion-related recombination suppression and the extenet of gene conversion on the Z chromosome within long-tailed finch subspecies.

References
Johnston SE, Huisman J, Pemberton JM (2018) A genomic region containing REC8 and RNF212B is associated with individual recombination rate variation in a wild population of red deer (Cervus elaphus). G3: Genes, Genomes, Genetics, 8, 2265-2276.

Stapley J, Feulner PGD, Johnston SE, Santure AW, Smadja CM (2017) Variation in recombination frequency and distribution across Eukaryotes: patterns and processes. Philosophical Transactions of the Royal Society, 372: 20160455

Hooper DM, Griffith SC, Price TD (2019) Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone. Molecular Ecology, 28, 1246-1262.

Griffith SC, Hooper DM (2017) Geographical variation in bill colour in the Long-tailed Finch: Evidence for a narrow zone of admixture between sub-species. Emu, 117, 141-150

Qualifications

We are looking for a candidate who:

• holds a Master degree (or will graduate before appointment date) with distinction and one year of research during the Masters (see: https://www.mq.edu.au/(...)degrees/how-to-apply ) in a relevant field, such as Evolutionary Biology
• is curiosity driven and passionate about fundamental research in the context of genomics and senescence
• has previous experience of bird ringing and conducting fieldwork in harsh environments (training will be provided)
• has strong quantitative skills in statistics and bioinformatics (training will be provided)
• has experience in extracting and analysing data from databases (e.g. Access) or large datasets (training will be provided)
• is a team player, willing to work with a diverse group of researchers and technicians, and can also work independently
• has strong communication skills and is motivated to disseminate results to both scientific peers and a broad audience
• is proficient in the English language (https://www.rug.nl/(...)ion/english?lang=en; https://www.mq.edu.au/(...)degrees/how-to-apply )
• is strongly motivated to obtain a PhD degree.

Organisation

We offer 1 full scholarship for a PhD project on recombination rates using long-term datasets of Seychelles warblers and long-tailed finches. This is a double-degree/cotutelle position at the University of Groningen, The Netherlands, and Macquarie University, Sydney, Australia.

Organization
Groningen Institute for Evolutionary Live Sciences (GELIFES), Faculty of Science and Engineering, invites applications for a fully-funded, scholarship PhD position in its Behavioural and Physiological Ecology group. This is a double-degree with the Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University.

University of Groningen (RUG)
Founded in 1614, the University of Groningen enjoys an international reputation as a dynamic and innovative center of higher education offering high-quality teaching and research. Flexible study programme and academic career opportunities in a wide variety of disciplines encourage the 32,000 students and researchers alike to develop their own individual talents. Quality has been our top priority for over four hundred years, and with success: the University is currently in or around the top 100 on several influential ranking lists.

GELIFES, Faculty of Science and Engineering, RUG
The Groningen Institute for Evolutionary Life Sciences (GELIFES), one of the larger institutes of the Faculty of Science and Engineering (FSE), fills a special niche in the life sciences by covering and integrating mechanistic, evolutionary and ecological approaches, aiming to understand adaptation on all levels of biological organization. Researchers pursue fundamental questions while collaborating with partners from nature conservation, industry, medicine and other realms of society. Our research fields include ecology, conservation biology, evolutionary biology, behavioural biology, chronobiology, genetics and genomics, neurobiology, physiology and theoretical modelling, using a wide array of research tools.

Macquarie University (MQ)
Sydney is a vibrant global power city rated in the world’s top-ten for economy, research and development, cultural interaction, live-ability, environment, and accessibility. Macquarie University is a major research-based institution situated in the heart of Sydney’s high technology precinct. It is considered one of Australia’s best universities and is rated among the top 1% of universities globally. Macquarie is a University engaged with the real and often complex problems and opportunities that define our lives. Since our foundation 54 years ago, we have aspired to be a different type of University. Over the years, we’ve grown to become the centre of a vibrant local and global community.

Department of Biological Sciences, Faculty of Science and Engineering, MQ
The Department of Biological Sciences is a vibrant community of teachers, researchers, professional staff and students working across a wide range of disciplines including animal behaviour, climate change, conservation, ecology, evolution, genetics and genomics, and physiology. The department’s commitment to research-led teaching ensures our students graduate with a broad base in contemporary biological thought, a passion for life-long learning and strong foundations for a career in the biological sciences and related areas.

Conditions

The position is offered within the RUG PhD Scholarship Programme. This programme is issued by the Dutch Ministry of Education, Culture, and Science (OCW) within the framework of the national PhD Scholarship Programme. The double-degree/cotutelle PhD scholarship student will receive a scholarship (stipend) of € 2,249 per month (gross) from the University of Groningen for the first part of the PhD (from the start date until 31 August 2024). This amount is adjusted annually on the basis of the CBS consumer price index. PhD scholarship students are not employed by the university. PhD scholarship students therefore have different rights, obligations, and a different income than employed PhD candidates. Please consider the terms and conditions of the PhD Scholarship Programme on the following website: https://www.rug.nl/(...)ditions-application/

Macquarie University offer a Cotutelle iMQRES Scholarship, for the last two-years of the PhD, from 1 September 2024. The Cotutelle scholarship comprises the equivalent of a full-fees award and stipend for the normal full-fee paying period up to 2 years. Scholarship holders will be expected to have submitted their thesis for examination by the end of that period. The scholarships will comprise a full-fees awards and a stipend paid at the current RTP stipend rate for 2021 (AUD 28,597 per annum) and indexed in future years.

Application

The selection procedure will proceed in three stages:

1. Application (before 8 August 2022)
2. Assessment by selection committee (August 2022)
3. Development of a full research proposal (before 1 September 2022)

1. Application
You can upload your complete application, in English until 7 August 11:59pm / before 8 August 2022 Dutch local time (CEST). Combine all required documents in a single PDF file and upload it via the online application form (click on 'Apply' below on the advertisement on the university website to access the application form). Please use the following format to complete your application file:
a) Title page (1 page max.):
• Name of the applicant
• MSc degree and university
• Intended starting date (1 November 2022, EU candidates; 1 January, 2023 non-EU candidates / candidates not already in possession of an NL residency permit)
b) Cover letter (1 page max.): a letter introducing yourself, describing your motivation and qualifications to conduct this scientific research, and your expectations of the PhD programmec) CV (2 pages max.)
d) Academic records and a certified copy or scan of your MSc diploma (or equivalent; provide a certified University letter stating when your graduation will be between the application deadline and start of the project)
e) Proof of sufficient competence in English (https://www.rug.nl/(...)sion/english?lang=en & https://www.mq.edu.au/(...)degrees/how-to-apply )
f) Names and contact details of two academic references
g) Initial research project idea: brief description of the research question(s) that you wish to address with respect to the advertised topic and your approach to address the research question(s) (500 words max.).
Applications that do not satisfy the requested format will not be taken into consideration.

2. Interviews
The application files of candidates will be assessed by the supervisors, using the following criteria:
1. qualifications of the candidate: grades, research experience and motivation
2. the research proposal: quality, originality, and feasibility
3. the admission requirements of the RUG Graduate School of Science and Engineering and MQ.
The highest ranked candidates will be invited to an interview with the supervisors. Interviews will take place in August 2022.

3. Development of a full research proposal
On the basis of the observed qualifications of the candidates, the quality and originality of the candidates’ initial research project idea, and the fit with the supervisors’ ongoing research, the supervisors will invite one candidate to develop their initial project idea into a full research proposal of approximately 1500-2000 words (excluding references). The proposal must include:
• Introduction, importance, and state of the art
• Main goal(s) and research question(s)
• Approach and methods
• Feasibility, research budget and timeline.

A final decision will then be reached.

The University of Groningen strives to be a university in which students and staff are respected and feel at home, regardless of differences in background, experiences, perspectives, and identities. We believe that working on our core values of inclusion and equality are a joint responsibility and we are constructively working on creating a socially safe environment. Diversity among students and staff members enriches academic debate and contributes to the quality of our teaching and research. We therefore invite applicants from underrepresented groups in particular to apply. For more information, see also our diversity policy webpage: https://www.rug.nl/(...)rsity-and-inclusion/

Our selection procedure follows the guidelines of the Recruitment code (NVP): https://www.nvp-hrnetwerk.nl/sollicitatiecode/ and European Commission's European Code of Conduct for recruitment of researchers: https://euraxess.ec.europa.eu/jobs/charter/code

Macquarie University, is committed to providing a working environment where each individual is valued, respected and supported to progress. Our priority is to ensure culture, policies and processes are truly inclusive and that no-one is disadvantaged on the basis of their Aboriginal and Torres Strait Islander identity, gender, culture, disability, LGBTIQA+ identities, family and caring responsibilities, age, or religion. We encourage everyone who meets the selection criteria and shares Macquarie University’s values of scholarship, empowerment and integrity to apply. Learn more about our progress towards Equity, Diversity and Inclusion: https://staff.mq.edu.au/(...)ersity-and-community .

Timeline
Deadline for application: before 8 August 2022
Interviews: August 2022
Start of the position: 1 November to 1 January 2022, EU candidates; 1 January, 2023 non-EU candidates / candidates not already in possession of a Dutch residency permit
Duration of funding: 44-46 months, dependent on start date

Unsolicited marketing is not appreciated.

Information

For information you can contact:

• Prof. Hannah Dugdale, [email protected]
• Prof. Simon Griffith, [email protected]
• Dr Susan Johnston, [email protected]

Please do not use the e-mail address(es) above for applications.

Apply