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QUADRAT DTP: Genome-wide diversity and demographic history of relict island populations of rodents


   School of Biological Sciences

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  Prof Stuart Piertney, Dr S Helyar, Dr A Douglas  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Conservation genetics theory predicts that when a few founding individuals colonise a vacant habitat they will experience a reduction in genetic diversity through the effects of genetic drift which can compromise the viability of the population and limit its capacity to adapt to the new environmental conditions. Such theory however is somewhat difficult to reconcile with the numerous examples we know of where invasive species have rapidly adapted and spread following introduction, or where small island populations have persisted over long time periods despite being genetically depauperate. Do these suggest that the tenet that substantial genetic variation is necessary for population persistence is wrong? Or does it highlight a complex interplay between how genetic variation erodes across the genome and the relationship this has with phenotypic traits that are adaptively important and ecological meaningful in insular populations?  

This PhD project will examine these issues in three parallel rodent study systems comprising brown rats (Rattus norvegicus), black rats (R. rattus) and water voles (Arvicola amphibius) that have been marooned as island relict populations either around the UK or the South Atlantic.  

The student will use state-of-the-art, long-read DNA sequencing approaches to characterise the genome-wide landscape of genetic diversity for multiple individuals of each of the three species. These data will then be used to reconstruct the demographic history of the populations, examine how genetic diversity has been eroded across the genome according to gene function and the effects of selection, and identify any novel genomic features that could explain ecological success. A comparison of patterns both within and between species will then enable the development of a suite of applied genomic assays that can be used for predicting and enhancing population persistence in species of conservation concern.  

The project offers outstanding training opportunities in the very latest genomics techniques and bioinformatic and evolutionary analyses, coupled with a programme of broad core and generic skills development that is central to the Quadrat DTP training programme. The student will become part of a dynamic and vibrant multidisciplinary research group and broader postgraduate community, plus have the opportunity to make a major contribution to our understanding of fundamental issues in conservation genetics and species management. 

Candidate Background: The successful candidate should have experience with standard molecular biology procedures (PCR, gel elecrophoresis, genotyping). A background and interest in conservation genetics and demonstrable science communication experience (both spoken and written). Experience using R, Python or equivalent to undertake basic bioinformatic or population genetic analyses is desirable.

More project details are available here: https://www.quadrat.ac.uk/quadrat-projects/

How to apply: https://www.quadrat.ac.uk/how-to-apply/ 


Funding Notes

QUADRAT studentships are open to UK and overseas candidates. Funding covers:
• A monthly stipend for accommodation and living costs, based on UKRI rates (currently £17,668 pa for 2022/23, updated annually)
• Fees (home rate tuition fees and/or fee waiver for overseas fees, where applicable)
• Research and training costs
For further information before applying please check full funding and eligibility information: https://www.quadrat.ac.uk/funding-and-eligibility/

References

1. Piertney SB, Black A, Watt L, Christie D, Poncet S, Collins MA (2016) Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia. Journal of Applied Ecology, 53, 332-339.
2. Gavan MK, Oliver MK, Douglas A, Piertney SB (2015) Gene dynamics of toll-like receptor 4 through a population bottleneck in an insular population of water voles (Arvicola amphibius). Cons Genetics 16, 1181–1193.
3. Oliver MK, Piertney SB (2012) Selection maintains MHC diversity through a natural population bottleneck. Molecular Biology and Evolution 29, 1713-1720.
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