Overview

Project Highlights:

You will:

  • Answer questions about fundamental processes that drive the evolution and diversification of gene expression, and genome structure and function.
  • Investigate the functional control of sex determination in a highly important, but little studied group of animals, Crustacea.
  • Gain invaluable skills in bioinformatics and the analysis of ‘big data’ from next generation sequencing, and present your research at national and international conferences.

Overview

The evolution of separate sexes - males and females (dioecy) – sets in train evolutionary conflicts between those genes that benefit females and those that benefit males. Conflict resolution is thought to arise in two ways, either by the evolution of sex chromosomes or the evolution of differential gene expression (Vicoso et al., 2013).

In this PhD you will use a novel approach and a model system developed by the supervisory team (Mathers et al., 2013a, Mathers et al., 2013b, Mathers et al., 2015) - the tadpole shrimp, (Triops sp.), a crustacean commonly kept as a pet - to shed light on this fundamental issue. You will investigate gene expression changes that have occurred recently during switches from dioecy to hermaphroditism. This causes a shift from selection optimising male and female function in separate individuals (high conflict) to selection optimising male and female function together in the same individual (low conflict). Your research will illuminate the selective mechanisms – such as antagonistic selection – that are hypothesised to underpin the evolution of sex differences (Bedhomme et al., 2009).

We have shown there are multiple independent evolutionary transitions between separate sexes (dioecy) to individuals with male and female function (hermaphrodites) in tadpole shrimps (Triops) (Zierold et al., 2007, Mathers et al., 2013a) which allows tests in multiple independent lineages and provides statistical robustness.

Your research will build upon work that has shown sex is genetically determined (Mathers et al., 2015), that has developed sex linked markers, and identified sex linked scaffolds in the three genomes (male, female and hermaphrodite) we have sequenced and assembled (unpublished).

You will develop functional molecular tests – such as gene expression knockdown with RNA interference – to investigate sex determination. Sex determination is poorly understood in crustaceans, an important gap in the wider understanding of the evolution of sex determination (Kato et al., 2011).

Figure 1: :Left: A male Triops cancriformis. Right: a phylogeny of Notostraca, an ancient crustacean order with only two genera Triops and Lepidurus.  Blue lines show ancestral dioecy (separate males and females). Orange lines show repeated and independent evolution of self-fertilising hermaphrodites (Mathers et al. 2013a). Notostraca are an excellent system to understand the genomic impact of sexual mode switching.

Methodology

You will rear Triops in the lab and extract both RNA and DNA.

You will measure differential expression of genes using next generation RNA sequencing analysis of replicate samples of males and females (dioecious pop.) and hermaphrodites at different developmental time points.

You will assemble transcriptomes by alignment to aassembled genomes and perform differential expression analysis. You will analyse gene ontology of differentially expressed genes.

You will analyses gene expression change in sex specific region genes identified in silico from the annotated genome in conjunction with known sex-specific RAD markers (Mathers et al., 2015).

You will develop RNAi knockdowns to test models of sex determination.

Training and Skills

Bioinformatics skills are essential in ‘big data’ modern biology, especially evolutionary and environmental biology. You will gain highly transferable skills in: biological computing and programming (e.g. PERL, Python, R), handling next generation sequencing data in a Linux environment, transcriptome assembly, molecular evolutionary analysis, and manuscript preparation and giving presentations.

In addition to CENTA training you will receive tailored training from:

  • Supervisors directly
  • Workshops offered Leicester’s Biostatistics and Bioinformatics Support Hub (BBASH)
  • University of Leicester courses (e.g. R)
  • By taking elements of Leicester’s Bioinformatics MSc (e.g. Python)

Timeline

Year 1: Familiarisation with the literature, sample collection, Triops husbandry, RNA extraction, RNA sequencing. Development of RNAi knockdown protocols. Bioinformatics skills development.

Year 2: Differential gene expression analysis of Triops species. Investigation of candidate sex determination genes. Knockdown experiments.

Year 3: Analysis of genome position effects. Comparative analysis of Triops differential gene expression. Analysis of candidate gene knockdown experiments. Manuscript preparation / thesis preparation.

 

Partners and collaboration (including CASE)

You will benefit from the complimentary expertise and the strong and established supervisory team of Hammond, Mallon and Gomez.

Dr Africa Gomez (Hull) is an evolutionary biologist, an expert on Triops and a long-time collaborator of Dr Hammond. Gomez and Hammond successfully supervised a NERC CASE PhD student (Dr T. Mathers, 3 papers, currently postdoc at the Earlham Institute) and have collaborated on the genome sequencing of Triops cancriformis. Mallon and Hammond have supervised collaboratively a NERC funded PhD student (Mark Harrison, currently a postdoc at University of Muenster, 2 papers, 2 in review) that used RNAseq (Harrison et al., 2015, Price et al., 2018), the primary research method used in this project.

Further Details

Please contact Dr Rob Hammond, University of Leicester.

Email: rh22@le.ac.uk

Phone: 0116 252 5302

Website: https://www2.le.ac.uk/departments/genetics/people/hammond