Evolutionary genomics under sexual and clonal reproduction in hybrid wild grasses

Evolutionary genomics under sexual and clonal reproduction in hybrid wild grasses

Project Description

Supervisors

Dr Jose De Vega, Earlham Institute

Professor Anthony Hall, Earlham Institute

Dr Rafal Gutaker, Royal Botanic Gardens, Kew

 

Scientific Background

Interspecific hybridisation is a common mechanism of diversification in plants, unlike in animals, largely because plants can overcome hybrid sterility through chromosome doubling, resulting in polyploid plants. Hybridisation and polyploidisation trigger genome-wide instability and reprogramming, manifesting as extensive structural and epigenetic variation, a phenomenon known as “genomic shock”. Apomixis, a form of asexual reproduction via clonal seed production, is often found associated with interspecific hybridisation. It is suggested as a transitional trait that can act as a “safety net” between hybrid formation and genomic stabilisation.

The evolutionary implications of apomixis remain unresolved despite its widespread occurrence across all major plant groups (spanning over 300 genera): While apomictic asexual lineages can potentially benefit from fixed heterozygosity, potential heterosis, and the preservation of well-adapted genotypes, they lack the genetic recombination necessary for adaptive evolution through natural selection.

This project aims to investigate how apomictic reproduction influences genomic diversity, regulatory dynamics, and evolutionary adaptability compared to sexual reproduction in natural (wild) plant populations. We will address two questions: (1) Does apomixis act as a transitional “safety net” mechanism post-shock that enables hybrid persistence and genomic stabilisation?; (2) Does apomixis constrain the long-term adaptability and evolutionary potential of the lineage?

 

Research Methodology

This project will investigate the evolutionary trade-offs of apomixis using existing transcriptomic and marker-based data, alongside new whole-genome resequencing, from hundreds of closely related sexual, apomictic, and hybrid accessions within the Urochloa (syn. Brachiaria) species complexes. Analyses will include population genomics, gene dosage and expression analysis, admixture and introgression analysis, and epigenomic and structural variation analysis.

 

Training

You will develop a broad set of skills in computational biology, genetic analysis, bioinformatics, and scientific writing. You will also gain expertise in evolutionary biology, plant sciences, and statistics. There is potential to explore fundamental molecular and horticultural techniques. Additionally, you will participate in both external and internal bioinformatic training courses and attend and present at conferences, local seminars, department and institute groups, and journal clubs.

 

Person Specification

We are looking for a highly motivated individual with a strong interest in evolution and genomics, and a basic understanding of R or Python.

Acceptable first degree subjects: A degree related to Biological Sciences, Environmental Sciences, or Bioinformatics.

Project code: DEVEGA_EI_ARIES26

References

  • Higgins et al. (2022), Diverged subpopulations in tropical Urochloa (Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution, Annals of Botany, 130: 657–669, https://doi.org/10.1093/aob/mcac115
  • Ryan et al. (2024), A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition. G3, 15: jkaf005, https://doi.org/10.1093/g3journal/jkaf005
  • Cervantes-Diaz et al. (2024), Ecological and evolutionary implications of hybridization, polyploidy and apomixis in angiosperms. Botany Sciences, 102: 3583, https://doi.org/10.17129/botsci.3583
  • Hijsgaard & Horandl (2019), The Rise of Apomixis in Natural Plant Populations. Frontiers in Plant Science, 10: 358, https://doi.org/10.3389/fpls.2019.00358
  • Kistler et al. (2025), Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation. Science, 387: 6738. https://doi.org/10.1126/science.adq0018

Key Information

  • This studentship has been shortlisted for funding under the UKRI NERC DLA funding scheme and will commence on 1 October 2026. The closing date for applications is 23:59 on 7 January 2026.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a fully-funded studentship, which covers fees, maintenance stipend (£20,780 p.a. for 2025/26) and a research training and support grant (RTSG). A limited number of studentships are available for international applicants, with the difference between 'home' and 'international' fees being waived by the registering university. Please note, however, that ARIES funding does not cover additional costs associated with relocation to, and living in, the UK, such as visa costs or the health surcharge.
  • ARIES postgraduate researchers (PGRs) benefit from bespoke training and ARIES provides £2,500 to every student for access to external training, travel and conferences, on top of all Research Costs associated with the project. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside non-academic experience, and our recruitment process considers potential with the same weighting as past experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis. International applicants should check whether there are any conditions of visa or immigration permission that preclude part-time study. All advertised project proposals have been developed with consideration of a safe, inclusive and appropriate research and fieldwork environment with respect to protected characteristics. If you have any concerns, please contact us.
  • For further information, please contact the supervisor. To apply for this Studentship, follow the instructions at the bottom of the page or click the 'apply now' link.
  • ARIES is required by our funders to collect Equality and Diversity Information from all of our applicants. The information you provide will be used solely for monitoring and statistical purposes; it will remain confidential and will be stored on the UEA SharePoint server. Data will not be shared with those involved in making decisions on the award of Studentships and will have no influence on the success of your application. It will only be shared outside of this group in an anonymised and aggregated form. You will be asked to complete the form by the University to which you apply.
  • ARIES studentships are subject to UKRI terms and conditions. Postgraduate Researchers are expected to live within reasonable distance of their host organisation for the duration of their studentship. Please see https://www.ukri.org/publications/terms-and-conditions-for-training-funding/ for more information.

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Apply now via the  University of East Anglia Application Portal