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Hard-wired for success? Unravelling genomic signatures in pollinators.


Project Description

Many pollinator species, recognised as essential for ecosystem function, are undergoing rapid declines. One recent exception is the ‘Tree Bumblebee’ Bombus hypnorum: expanding its range into and across the UK in <20 years, it is now one of our most common species.

Building on previous work from the supervisory team, and in collaboration with the Earlham Institute, this project will investigate key genomic differences between this and other bumblebee (Bombus) species to substantially improve our understanding of the factors contributing to its success, along with the declines of others. The project’s focus is a genomic comparison of Bombus species from within the UK and continental Europe. Initial work has identified genomic regions of interest in B. hypnorum that may be indicative of its ability to adapt to anthropogenically altered landscapes. However, current data are preliminary and lack essential phylogenetic comparison.

This is a timely and exciting opportunity to generate a highly novel, and substantial, genomic dataset to test hypotheses as to whether the observed genomic differences are unique to B. hypnorum, or shared among Bombus species (some evidence suggests elevated resilience in the wider Pyrobombus sub-genus). In addition to fulfilling the specific aims, the data generated will offer the student significant scope to guide the project's further direction through characterisation of genomic signatures and differences across this important pollinator group.

The project will equip the successful student with state-of-the-art genomic techniques as well as bioinformatic and modelling skills that are highly transferable and increasingly essential across a wide range of academic and applied biological disciplines. The student will also gain important soft skills (e.g. communication, team working, problem solving). He/she will be based in Plymouth, spending short periods at the other Institutions as relevant.

The successful candidate will have a biology-based degree, an academic interest in evolutionary ecology, and be enthusiastic about pursuing a laboratory- and computer-based project. Ideally, he/she will have some basic molecular ecology experience (e.g. DNA extraction, PCR) and interest in genetic and evolutionary analysis. Experience of genome sequencing and bioinformatics is not essential as full training will be provided.

Supplementary information

The project unites two research groups working on the UK colonisation of Bombus hypnorum: Professor Bourke’s group (UEA;1,2) and Drs Knight/Ellis group (UoP;3). Both groups have substantial research expertise in bumblebee and related research (4-11), complemented by the evolutionary genomic expertise of Dr Haerty (Earlham Institute;12-15). The assembled team has a demonstrable record of high impact publications (e.g. Molecular Ecology, Scientific Reports, Nature).

Key findings of our combined previous research are that B. hypnorum has colonised the UK from continental Europe recently via multiple routes, and that this is ongoing. This raises two related unanswered questions: why has this species not colonised previously? and why has it been so successful given concurrent declines in other Bombus species?

Several potential factors might underpin the influx of B. hypnorum from continental Europe including life history and social behaviour (currently the focus of a PhD project at UEA), climate change/changes in transport links (investigated in a UoP PhD project commencing Sept 2019), and/or adaptive predisposition or shift.

This project focuses on the identification of genomic signatures associated with an adaptive predisposition or shift conferring a competitive advantage on B. hypnorum and/or a wider taxonomic group (16,17) over other UK natives, through whole genome comparisons. It builds on the team’s recent partial genome scan results (3) suggesting possible selection signatures on particular genomic regions that may provide this species with an adaptive advantage (e.g. ion channel receptors, which have been linked to pesticide resistance (3,16)).

Comprehensive genomic coverage of both B. hypnorum and a range of other UK species is required in order to determine whether these differences are shared across Bombus or specific to B. hypnorum and/or its sub-generic group (16,17). To address this, the student will sequence whole Bombus genomes from each of the 5 major subgenera present in the UK and continental Europe (4 belonging to Pyrobombus, including B.hypnorum; 2 from Thoracobombus; 1 each from Bombus, Melanobombus and Megabombus). Samples will be prepared for sequencing in the laboratory at UoP, and processed (as standard) on an external Illumina platform. Two Bombus reference genomes are available for alignment (B. terrestris and B. impatiens), greatly easing bioinformatic assembly. The project will also greatly benefit from the genomic resources for diverse Bombus species produced at the Earlham Institute as part of the Darwin Tree of Life project. Genome analysis pipelines are already in place (3) with potential for further development by the student.

The substantial and highly novel dataset generated will allow significant scope for the student to investigate other comparative genomic changes (e.g. protein structure modelling).The student will benefit from the input and networks of three major Institutions and develop a range of technical and academic skills that are in high demand in both academic and applied biological disciplines.

How to apply

You can apply via the online application form which can be found at: https://www.plymouth.ac.uk/student-life/your-studies/research-degrees/applicants-and-enquirers and click ‘Apply now’.

Funding Notes

The studentship is supported for 3.5 years and includes full home/EU tuition fees plus a stipend (2019-20 rate is £15,009 per annum, 2020-21 rate to be confirmed).The studentship will only fully fund those applicants who are eligible for home/EU fees with relevant qualifications.

References

Crowther et al (2014); 2. Crowther et al (2019); 3. Huml et al (in revision); 4. Knight et al (2005); 5. Knight et al (2009); 6. Ellis et al (2006); 7. Ellis et al (2013); 8. Bourke (2019); 9. Carvell et al (2017); 10. Zanette et al (2012); 11. Charman et al (2010); 12. Johnson et al (2018); 13.Macaulay et al (2015); 14. Haerty & Ponting (2014); 15. Li et al (20130); 16. Theodorou et al (2018); 17. Arbetman et al (2017); 18. https://nbnatlas.org/

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