PhD Scholarship Recombination rates in Seychelles warblers & long-tailed finches

We are looking for a student who wishes to design their own PhD research project researching recombination rates. You will be supervised by Hannah Dugdale (RUG; https://hannahdugdale.wordpress.com), Susan Johnston (University of Edinburgh, https://sejohnston.com/), and Simon Griffith (MQ; https://griffithecology.com). The work on the Seychelles warblers will be in collaboration with David S Richardson (University of East Anglia, UK; https://people.uea.ac.uk/david_richardson) and on the long-tailed finches with Daniel Hooper (Columbia University, https://www.danielmarchooper.com/people).

This is a double degree at RUG and MQ. For the first two-years you will be based at RUG and embedded in the Seychelles Warbler Project (http://seychelles-warbler-project.group.shef.ac.uk). You will conduct fieldwork in the Seychelles for a minimum of two seasons (up to 3 months per season), with a COVID-19 contingency plan. For the second two-years you will be based in Australia on the MQ campus. You will be part of a team of PhD students, post-docs, and staff who are using long-term individual-based datasets to improve understanding of life-history evolution.

As a PhD scholarship student, you will develop your own research project in consultation with the associated supervisors. You will conduct independent and original scientific research, report results via peer-reviewed publications, conference presentations, and ultimately a PhD thesis. The PhD thesis has to be completed within four years. Being part of a cutting-edge research programme, you will receive training in the form of hands-on instruction, advanced courses, summer/winter schools, as well as complementary workshops on generic research and transferable skills. Special attention is paid to training activities directed towards your future (academic or non-academic) career after the PhD trajectory, in the context of the RUG’s Career Perspective Series, and the Research Training Certification Program at MQ.

Project
Recombination is the crossing over of maternal with paternal chromosomes during reproduction. Recombination can generate and break-up both beneficial and detrimental genetic variation combinations in the resulting offspring. Novel genetic combinations may allow populations to respond to change, with fitness consequences, and can also be important in speciation. We have however a limited understanding of the causes and consequences of vartiation in recombination rates within and between individuals, and at speciation level. You will design your project to investigate these effects.

In the Netherlands, you will use the long-term Seychelles warbler dataset to address this question. Seychelles warblers are cooperative breeders and we have detailed life-history data of over 2,000 birds, spanning more than 30 years. We have whole genome sequencing data from 1,800 of these individuals at 5-15x coverage. Potential research questions are do recombination rates differ between individuals and are these differences heritable, and what are the fitness consequences of these differences.

In Australia, you will work on the recombination landscape of the Z chromosome in long-tailed finches, using a haplotagging dataset. Most of the Z chromosome appears to be a recombination desert in long-tailed finches but there are large inversions segregating. Our inference about the process behind the supposed recombination desert on the long-tailed finch Z chromosome comes from high-linkage disequilibrium between subspecies and the low genetic diversity within subspecies within the interior of the Z chromosome. You will investigate the effect of inversion-related recombination suppression and the extenet of gene conversion on the Z chromosome within long-tailed finch subspecies.

References
Johnston SE, Huisman J, Pemberton JM (2018) A genomic region containing REC8 and RNF212B is associated with individual recombination rate variation in a wild population of red deer (Cervus elaphus). G3: Genes, Genomes, Genetics, 8, 2265-2276.

Stapley J, Feulner PGD, Johnston SE, Santure AW, Smadja CM (2017) Variation in recombination frequency and distribution across Eukaryotes: patterns and processes. Philosophical Transactions of the Royal Society, 372: 20160455

Hooper DM, Griffith SC, Price TD (2019) Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone. Molecular Ecology, 28, 1246-1262.

Griffith SC, Hooper DM (2017) Geographical variation in bill colour in the Long-tailed Finch: Evidence for a narrow zone of admixture between sub-species. Emu, 117, 141-150