This studentship aims to gain a better understanding of fundamental processes of genome evolution that remain poorly understood. The project will investigate the role of transposable elements (TEs) in evolutionary diversification following whole genome duplication (WGD), using salmonid fishes as an ideal study system due to the presence of an ancestral WGD event that has had a major impact on genome evolution and been linked with lineage diversification (e.g. Lien et al. 2016; Robertson et al. 2017).
We will test the hypothesis that TEs have been instrumental agents in reshaping genetic and epigenetic evolution following WGD, promoting adaptation. The work will involve comparative genomic analysis of multiple fish species and investigate several levels of genome-wide functional regulation (Macqueen et al. 2017) to characterize expression changes in duplicated genes, which will be associated with TE sequence evolution and changes in epigenetic status. The analyses will focus around embryogenesis and early development.
Additional information: This PhD is embedded within a Norwegian research project ‘TRANSPOSE: Transposable elements as agents of genome evolution and adaptation following a recent whole genome duplication’. TRANSPOSE is a 5 year project and supervisor Macqueen is a collaborator. The student will benefit from interactions with the world-leading network of salmonid researchers involved in TRANSPOSE, including scientists based at the Norwegian University of Life Sciences that helped deliver the Atlantic salmon genome (see Lien et al. 2016).
Training opportunities: The student will be trained to apply leading-edge genomics technologies (e.g. RNA-seq and ATAC-seq), and deal with omics datasets using advanced bioinformatic and statistical tools. They will also receive training in fish development, molecular biology, comparative analysis, evolutionary genomics and phylogenomics.
The candidate: we are seeking a strong student with interests and preferably experience in any of the following or related fields: bioinformatics, genomics, development and evolution. Candidates will have at least an upper 2:1 degree in the biological sciences (or a closely-related field) and preference will be given to individuals with a relevant Master’s degree, or other relevant experience. The successful student will be required to travel outside the UK for fish sampling, potentially for extended periods.
Please apply for admission to the ’Degree of Doctor of Philosophy in Biological Science’ to ensure that your application is passed to the correct School for processing.
Please provide a copy of the degree certificate and transcript for each previous degree undertaken, a copy of your English language proficiency certificate (if relevant), and contact details of two referees who can comment on your previous academic performance (at least one should be from your current degree programme). References will be requested if you are selected for interview. Incomplete applications will not be considered.
Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS (2016). The Atlantic salmon genome provides insights into rediploidization. Nature. 533, 200-5.
Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escárate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop BF, Lien S, Maass A, Martin SAM, McGinnity P, Montecino M, Naish KA, Nichols KM, Ólafsson K, Omholt SW, Palti Y, Plastow GS, Rexroad CE, Rise MR, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM (The FAASG Consortium) (2017) Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics. 18: 484.
Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PW, Sandve SR, Macqueen DJ (2017) Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol. 18: 111.