We are seeking applicants for two fully-funded PhD positions as part of an exciting research project in evolutionary biology in the School of Biological Sciences at the University of Auckland.
The project is supported by a prestigious Marsden Fund grant from the Royal Society
of New Zealand (Royal Society Te Aparangi) to Drs. Nobuto Takeuchi, Austen Ganley, and Profs. Anthony Poole & Timothy Cooper.
One PhD position is in computational modelling (Takeuchi lab), and the other is in laboratory-based experimental bacterial evolution (Poole lab). Each position provides a stipend of NZD 33,825 per annum (tax exempt) for the full three-year PhD program as well as full university fees (for both national and international candidates).
The overall goal of the project is to understand what drives the evolution of reproductive divisions of labour (RDL), where sterile 'helpers' assist specialised 'reproducers' in transmitting genetic information. RDL has evolved repeatedly at vastly different biological scales. Examples include eusocial insects with queens and workers,
multicellular organisms with germline and soma cells, and cells with genomes and enzymes (enzymes provide catalysis, 'helping' genomes transmit genetic information). What drives the repeated evolution of RDL across different scales? Traditionally, it has been hypothesised that RDL increases group-level production efficiency because investment in a particular task brings accelerating returns - we call this the 'efficiency' hypothesis. However, our recent modelling work suggests that efficiency gains are not necessary for RDL to evolve [1]. Based on this, we propose an alternative hypothesis: that RDL evolves because of its ability to inhibit the evolution of 'cheaters' – individuals that avoid cooperation and replicate uncontrollably. We call this the cheater hypothesis. While the traditional efficiency hypothesis relies on system-specific explanations for how RDL increases production efficiency, the new cheater hypothesis is simple: it predicts RDL is beneficial under any conditions where cheaters can prosper and is, thus, independent of idiosyncrasies in different systems because cheating is known to occur across many systems and biological scales.
The goal of the two PhD projects is to test both efficiency and cheater hypotheses using complementary computational modelling and lab-based experimental evolution approaches. Specifically, the computational PhD student will use individual-based modelling to determine general conditions under which queen-worker RDL evolves to
inhibit cheater evolution. The experimental PhD student will undertake experimental evolution using E. coli to test both the cheater and efficiency hypotheses by quantitatively assessing the effects of RDL in a molecular-level system involving helper and reproducer plasmids.
Your role:
PhD position 1 (computational modelling):
Your role will be to implement individual-based models using a fast programming language, such as C++ and Java, run the models using Linux clusters, and analyse data generated by the models, with the goal of determining the general conditions under which queen-worker RDL evolves. You will also collaborate with experimental team members to identify parameters relevant to their experiments. You will obtain world-class training in modelling, designing research, writing papers, presenting your research at scientific conferences, and collaborating with team members. You will have ample opportunities to interact with multiple academics, including your main supervisor, Nobuto Takeuchi, and your co-supervisor, Austen Ganley, and other PhD students through regular meetings and retreats.
Post-graduate research experience in one of evolutionary theory, theoretical ecology, theoretical/mathematical biology, statistical physics, mathematical modelling, and/or any relevant fields is necessary, but project-specific training will be provided. Programming skills, a keen interest in quantitative and abstract thinking, and excellent academic communication skills are essential.
PhD position 2 (laboratory evolution):
Your role will be to first use molecular and synthetic biology approaches to build a plasmid-based RDL system and then use laboratory evolution approaches to examine whether the evolutionary dynamics of these systems are consistent with the efficiency hypothesis or the cheater hypothesis. You will obtain world-class training in synthetic biology, performing experimental tests of theoretical predictions, designing research, performing laboratory evolution experiments, writing papers, presenting your research at international scientific conferences, and collaborating with team members. You will have ample opportunities to interact with multiple academics, including your main supervisor, Anthony Poole, and your co-supervisor, Nobuto Takeuchi, and other PhD students through regular meetings and retreats.
Research experience in at least one of synthetic biology, laboratory evolution experiments, microbiology, and/or molecular genetics is necessary, but project-specific training will also be provided. Enthusiasm for working in an interdisciplinary team, strong troubleshooting skills, and excellent academic communication skills are also essential.
About us:
Dr. Takeuchi is a theoretical biologist interested in the evolution of biological complexity. His research group uses modelling and bioinformatics to study how biological systems accumulate information through evolution.
Prof. Poole has expertise in experimental evolution. His research group uses both experimental and computational methods study the early evolution of life. His lab is actively using experimental evolution coupled to genome sequencing, with the bacterium E. coli as the main model system, to test questions that relate to the first emergence of modern biological systems.
Our labs are based in the School of Biological Sciences situated on the University of Auckland's city campus in downtown Auckland. Auckland is the largest city in New Zealand. Sitting astride two stunning harbours, with parks, beaches, rainforests and mild winters, it is a vibrant, multicultural and multilingual city. The annual Global Liveability Index ranked Auckland in the world's top 10 liveable cities in 2024.
How to apply:
Please send applications
for PhD Position 1 (computational modelling) to Dr. Nobuto Takeuchi (nobuto.takeuchi@auckland.ac.nz)
for PhD Position 2 (experimental evolution) to Prof. Anthony Poole (a.poole@auckland.ac.nz)
by Sunday, September 8, 2024, in the following format:
1. A Curriculum Vitae,
2. A personal statement (750 words maximum) outlining (i) your interest in the position, (ii) what you hope to achieve from the PhD and (iii) your research experience to date,
3. Academic transcripts for all university course grades to date,
4. Contact details for two academic or professional referees (at least one academic).
We welcome informal enquiries about either project (please contact us at the email addresses listed above).
Reference
[1] Takeuchi & Kaneko. 2019 The origin of the central dogma through
conflicting multilevel selection. Proc. R. Soc. B. 286:20191359.
https://doi.org/10.1098/rspb.2019.1359
