*2x PhD studentships in animal immune system origins and evolution*

Applications are welcomed for two fully funded, four-year, full-time
PhD positions at University College Dublin, Ireland.

*PhD Project area*: Reconstructing animal immune system evolution.

*PhD supervisor*: Dr Anthony Redmond

*Proposed Start Date*: Early 2025

*Location*: School of Medicine, University College Dublin, Ireland

*Positions*: 2x 4-year, Full-time PhD studentships (One University
College Dublin Ad Astra PhD

Studentship and one Royal Society-Research Ireland PhD studentship).

*Stipend: * euro 22,000 per annum plus tuition fee waiver.

*Summary of Project(s)*: The immune system is a complex evolutionary
marvel. Although the system is very well studied in humans, and in some
key model organisms, the early formation of the animal immune system is
poorly understood. This has been complicated by a combination of issues,
including: i) poor availability of high-quality genomes for some of our
most distantly related animal relatives, ii) the fast-evolving nature of
immune genes rendering homology difficult to identify across large periods
of time, and iii) uncertainty in the relationships of the major animal
lineages. Fortunately, high-quality genome sequences are now available
for representatives of the major animal lineages, while combining wet
lab and 'omics' approaches means that genes responding to immune
challenges can be more readily identified, providing an unprecedented
opportunity to counteract the key issues outlined above.

Both studentships will involve collection and maintenance of
phylogenetically important marine invertebrates in the lab for use in
genome sequencing (where required) and analysis, and immune challenge
trials and transcriptomics, to identify the array of immune-associated
genes in key lineages. This will reveal both candidate novel immune genes,
as well as homologs of known immune genes found in traditional model
species. This approach will be paired with phylogenetic investigation
of immune genes from across animal diversity to guide reconstruction of
the key steps in immune system evolution.

The proposed projects are intertwined in approach and share the
overarching aim of understanding the origins and evolution of the animal
immune system, but diverge in that one studentship will focus on the
early evolution of the bilaterian immune system and the other on immune
evolution in non-bilaterian animals.

These interdisciplinary projects intersect evolutionary genetics,
invertebrate zoology, immunology, and bioinformatics. Appropriate
training and/or opportunities to gain experience will be provided in
skills spanning these areas, including in fieldwork and husbandry of
marine invertebrates, wet-lab immune challenges trials, as well as in
phylogenetics, bioinformatics and 'omics' techniques. The student
will have the opportunity to publish in leading scientific journals and
to attend international conferences.

*Research Team and Environment*: The successful candidates will join the
newly established Redmond lab in University College Dublin's School of
Medicine. The group focuses primarily on understanding the evolutionary
history of animals, with particular interests in genome evolution, immune
systems, and resolving the tree of life, as well as the development of
new methodological approaches that this research agenda calls for. Both
studentships will benefit from opportunities to contribute to other
projects as well as from planned local and international collaborations
to ensure the success of this project.

*Requirements Qualifications/Expertise*: Applications are sought
from inquisitive and dedicated candidates with interest in scientific
methodology and discovery. Candidates should have, or expect to soon be
awarded, a BSc (grade 2.1 or above), or an MSc in the area of biology
(especially: genetics, immunology, zoology or related fields) and/or
computer science.

*To apply for these positions*: Please send your CV, a cover letter, and
the contact details of at least two referees to anthony.redmond@ucd.ie
by 30th November 2024. Informal enquiries in relation to the position are
welcome and encouraged and should also be sent to this address. Applicants
will be considered for both studentships unless otherwise stated in the
cover letter.

*Relevant publications*:

Redmond, A.K., 2024. Acoelomorph flatworm monophyly is a long-branch
attraction artefact obscuring a clade of Acoela and Xenoturbellida.
*Proceedings
of the Royal Society B: Biological **Sciences*, 291 (2031).

Matz, H., Taylor, R.S., Redmond, A.K., Hill, T.M., Daniels, R.R., Beltran,
M., Henderson, N.C., Macqueen, D.J. and Dooley, H., 2023. Organized B cell
sites in cartilaginous fishes reveal the evolutionary foundation of
germinal centers. *Cell reports*, 42(7).

Redmond, A.K., Pettinello, R., Bakke, F.K. and Dooley, H., 2022. Sharks
provide evidence for a highly complex TNFSF repertoire in the jawed
vertebrate ancestor. *The Journal of Immunology*, 209(9), pp.1713-1723.

Tan, M., Redmond, A.K., Dooley, H., Nozu, R., Sato, K., Kuraku, S., Koren,
S., Phillippy, A.M., Dove, A.D. and Read, T., 2021. The whale shark genome
reveals patterns of vertebrate gene family evolution. *Elife*, 10, p.e65394.

Redmond, A.K. and McLysaght, A., 2021. Evidence for sponges as sister to
all other animals from partitioned phylogenomics with mixture models and
recoding. *Nature communications*, 12(1), p.1783.

Redmond, A.K., Zou, J., Secombes, C.J., Macqueen, D.J. and Dooley,
H., 2019. Discovery of all three types in cartilaginous fishes
enables phylogenetic resolution of the origins and evolution of
interferons. *Frontiers in immunology*, 10, p.467824.

Redmond, A.K., Macqueen, D.J. and Dooley, H., 2018. Phylotranscriptomics
suggests the jawed vertebrate ancestor could generate diverse helper and
regulatory T cell subsets. *BMC **Evolutionary Biology*, 18, pp.1-19.

Anthony Redmond <anthony.k.redmond@gmail.com>

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