Evolutionary genomics under sexual and clonal reproduction in hybrid wild grasses

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?

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.

Entry requirements

At least UK equivalence Bachelors (Honours) 2:1. English Language requirement (Faculty of Science equivalent: IELTS 6.5 overall, 6 in each category).

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

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