Project Description

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. 

This is a lab-based project suitable for a student with interests in conservation genetics and a background in zoology, evolutionary biology or genetics. The student will be based primarily at the University of Aberdeen working in Professor Stuart Piertney’s laboratory with input around bioinformatic analysis from Professor Alex Douglas. There will be frequent interactions with Dr Sarah Helyar at Queens’ University Belfast as well as periods of labwork as appropriate within her Belfast lab. Samples have already been collected, so there is no direct fieldwork requirement, but some opportunities to visit field sites.  The main activity will be around DNA sequencing and bioinformatic analysis, for which state-of-the-art facilities are available and full training will be provided. 

Essential & desirable candidate skills

Essential: Experience with standard laboratory molecular biology procedures (PCR, gel electrophoresis, genotyping). Background and interest in conservation genetics. Demonstrable science communication experience (both spoken and written). 

Desirable: Experience using R, Python or equivalent to undertake basic bioinformatic or population genetic analyses.   

Supervisors

Stuart Piertney

Primary Supervisor:

Profile: Stuart Piertney
Email: s.piertney@abdn.ac.uk
Institution: University of Aberdeen
Department/School: School of Biological Sciences

Sarah Helyar

Secondary Supervisor:

Profile: Sarah Helyar
Email: s.helyar@qub.ac.uk
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences

Alex Douglas

Additional Supervisor:

Profile: Alex Douglas
Email: a.douglas@abdn.ac.uk
Institution: University of Aberdeen
Department/School: School of Biological Sciences

References

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. 

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. 

Oliver MK, Piertney SB (2012) Selection maintains MHC diversity through a natural population bottleneck. Molecular Biology and Evolution 29, 1713-1720.  

Impact

The project will provide fundamental understanding of the interrelationships between demographic history, genome dynamics, individual fitness and population persistence. This can then be leveraged to help inform and address some key issues of major applied and societal importance, including but not limited to how we effectively manage populations of conservation concern, how we control the persistence and movement of non-native invasive species and how we can predict the emergence and spread of zoonotic diseases. 

Proposed Timetable

The 42-month project will be structured around the generation, characterisation and comparison of three core genome-wide DNA sequence datasets from three rodent systems – the water vole, black rat and brown rat. Samples have already been collected for all three species, allowing the student to really hit the ground running with analysis. There will be an initial period of 3-6 months for literature review, assimilation and synthesis, plus training in lab and bioinformatic skills. The main activities during the core part of the PhD will include obtaining long-read DNA sequence data for multiple individuals for each species and characterising levels of DNA variation across samples in relation to gene function, and environmental conditions. The project retains a level of flexibility for the student to develop any particular avenues of the research that find particularly interesting or fruitful, and offers creative scope in how data are analysed. There is an expectation that the student will engage in an active programme of science communication activities across a range of academic and non-academic audiences and end-users.

QUADRAT Themes

  • biodiversity

Partners

Not applicable at this time.

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