Two fully-funded PhD positions in bacterial experimental 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 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

Nobuto Takeuchi <nobuto.takeuchi@auckland.ac.nz>

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