Two fully-funded PhD positions in laboratory evolution and computational modelling at the University of Auckland, New Zealand 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 Apârangi) to Nobuto Takeuchi, Austen Ganley, and Timothy Cooper. One PhD position is in computational modelling, the other is in laboratory evolution. Each PhD position provides a stipend of NZD 33,825 per annum (tax exempt) for the full three-year PhD program (36 months) as well as full university fees (for both national and international candidates). The details are as follows (the same information with additional links is available at: https://www.findaphd.com/phds/project/two-fully-funded-phd-positions-in-laboratory-evolution-and-computational-modelling-at-the-university-of-auckland-new-zealand/?p169240 ) 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 and at vastly different biological scales. Examples include eusocial insects with queens and workers, multicellular organisms with germline and soma cells, ciliates with micronuclei and macronuclei, 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 work, 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 laboratory 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 use laboratory evolution to test both the cheater and efficiency hypotheses by quantitatively assessing the effects of RDL on a synthetic yeast system engineered to have a germ-soma distinction. The positions are open to candidates who have an MSc, BSc(Hons), or equivalent qualifying degree in a relevant discipline. 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 using computational tools, such as R and Python, 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/computational/systems/quantitative biology, theoretical population genetics, statistical physics, applied mathematics, and/or any relevant fields is necessary, but project-specific training will be provided. The ability to learn programming languages, 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 genetic and synthetic biology approaches to build additional yeast germ-soma systems 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 scientific conferences, and collaborating with team members. You will have ample opportunities to interact with multiple academics, including your main supervisor, Austen Ganley, 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, yeast biology, 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. Dr. Ganley is a genome biologist interested in molecular mechanisms that shape genome evolution. His research group uses both experimental and bioinformatics approaches to address important questions in genome evolution, principally using budding yeast as a model system. 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 2023. 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 (laboratory evolution) to Dr. Austen Ganley (a.ganley@auckland.ac.nz) by Wednesday, March 20, 2024, in the following format: (1) A Curriculum Vitae, (2) A personal statement (750 words maximum) outlining (i) your suitability for the position, (ii) what you hope to achieve from the PhD and (iii) your research experience to date, (3) Academic transcripts of 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). References: [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 "nobuto.takeuchi@auckland.ac.nz" (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)