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NERC GW4+ DTP PhD studentship: How have gene family duplications shaped the disparity and diversity of mammal clades?

  • Full or part time
  • Application Deadline
    Monday, January 07, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

This project is one of a number that are in competition for funding from the NERC Great Western Four+ Doctoral Training Partnership (GW4+ DTP). The GW4+ DTP consists of the Great Western Four alliance of the University of Bath, University of Bristol, Cardiff University and the University Exeter plus six Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology and Hydrology, the Met Office, the Natural History Museum and Plymouth Marine Laboratory. For further details, see https://nercgw4plus.ac.uk/

Supervisory team –

Lead Supervisor: Professor Matthew Wills, University of Bath, Milner Centre for Evolution
Co-Supervisor: Dr Araxi Urrutia, University of Bath, Milner Centre for Evolution
Co-Supervisor: Professor Martin Genner, University of Bristol, School of Biological Sciences

Project background -

Understanding the forces that shape global biodiversity patterns was identified as one of the 25 greatest challenges for Science in the 21st Century (1, 2). Some mammal clades are enormously diverse, while their sister groups (originating at the same time) are far less so (e.g., 1,500 species of rodents versus 80 species of rabbits, hares and their allies). Why is this, and what might these differences tell us about the likely responses of groups to the present biodiversity crisis? In this strongly inter-disciplinary project, we will investigate the possible role of Small Scale Duplications of genes (SSDs) in shaping patters of diversity, anatomical complexity and morphological disparity of mammals in deep time.

As noted by Ernst Haeckel, developmental trajectories tend to become more complex with macroevolutionary time. Increasing interdependencies between genes and systems, coupled with their co-option for multiple functions (pleiotropy), result in more deleterious collateral consequences of mutations. This predicts that aspects of bodyplan design may become arbitrarily ‘locked down’ (e.g., seven neck vertebrae in most mammals), and that evolutionary innovation will be commonest when genetic redundancy is highest.

Small Scale Duplications of genes (SSDs) increase the number of genes within a given gene family (gene family size, GFS), and are one way in which mammals may circumvent such pleiotropic constraints and facilitate innovation.

Project aims and methods -

The overarching objective is to understand the factors shaping the striking asymmetry of diversity within the tree of life, and within the mammals in particular. We will investigate the role of gene family duplications in this regard. However, the precise objectives and focus will depend upon the interests and aptitude of the student.

We will use annotated genome data from Ensembl and the Comparative Genomics database to map GFS onto large phylogenies. OrthoMCL groups will be used to investigate species with no Ensembl annotation. We will compile trait data from Dryad and Morphobank. We will identify ‘shifts’ in speciation rate and test for correlations between the rate of gene duplications, discrete morphological trait evolution and speciation rate.

We will differentiate single-branch rate shifts (e.g. rapid shifts in individual taxa) from shifts within clades (e.g. jumps to adaptive optima). We will model speciation, extinction, and trait evolution to account for variable sampling, evaluate different models of change (e.g. passive diffusion, early bursts, punctuation) and assess their fit to phylogenies via information criteria (e.g. Akaike; Bayesian), using a suite of R packages (e.g. Auteur; Bayou; Ape; Gieger; Motmot; BAMM; Phytools). If gene duplications underpin morphological evolution, branches with WGDs or higher GFS will have higher diversification rates, more morphological novelties and higher disparity than their sister clades.

Disparity will be quantified using discrete morphological data sampled from all aspects of anatomy (published repositories) and our own R scripts. Bodyplan complexity will be quantified using a variety of information statistics applied to both the serial differentiation of vertebrae and limb elements. Morphometric data will be collected where more nuanced shape quantification is needed (e.g. details of vertebrae, ribs, girdles and limbs.

Applications –

The project is suitable for anyone interested in macroevolutionary patterns, and wishing to pursue a career in bioinformatics, phylogenomics and big biological data.

Candidates should apply using the relevant University of Bath online application form: https://www.bath.ac.uk/study/pg/applications.pl#bio-sci

When completing the form, please state in the ‘Finance’ section that you wish to be considered for GW4+ DTP funding and quote the project title and lead supervisor’s name in the ‘Your research interests’ section. You may apply for more than one project if you wish but you should submit a separate personal statement for each one.

More information on how to apply may be found here:
https://www.bath.ac.uk/guides/how-to-apply-for-doctoral-study/

Anticipated start date: 30 September 2019.

Funding Notes

NERC GW4+ DTP funding is for 3.5 years and is open to UK and EU applicants who have been resident in the UK since September 2016. A limited number of studentships may be available for EU applicants not meeting the residency requirement.

A studentship will provide UK/EU tuition fees, maintenance in line with the UKRI Doctoral stipend rate (£14,777 per annum, 2018/19 rate) and a generous budget for research expenses and training.

References

1. Kennedy D & Norman C (2005) Science 309:75.
2. Pennisi E (2005) Science 309:90.
3. Hughes M, Gerber S, & Wills MA (2013) PNAS 110(34):13875-13879.
4. Oyston J, Hughes M, Gerber S, & Wills MA (2016) Ann Bot 117:859-879.
5. McShea D & Brandon RN (2010) Biology's First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems (University of Chicago Press, Chicago) p 170.
6. Adamowicz SJ, Purvis A, & Wills MA (2008). PNAS 105(12):4786-4791.
7. Wills MA, Briggs DEG, & Fortey RA (1998) Systemat Assoc Spec Vol 55:57-65.
8. Wills MA, Briggs DEG, & Fortey RA (1994). Paleobiology 20(2):93-130.
9. Ruta M, Angielczyk KD, Froebisch J, & Benton MJ (2013) Proc R Soc B 280(1768).
10. Davis KE, Hill J, Astrop TI, & Wills MA (2016) Nature Comm 7:13003.

How good is research at University of Bath in Biological Sciences?

FTE Category A staff submitted: 24.50

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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