Overview

Physically separate males and females – known as dioecy - has evolved many times [1] yet the selective and molecular mechanisms underpinning this change are not clearly understood.  This is because sex differences are often longstanding so disentangling cause and effect is tricky [2].

In this PhD project you will use a novel approach and a model system developed by the supervisory team [3-5], 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 and in the reverse sexual mode switch - from dioecy to hermaphroditism. This change in sexual mode causes a shift from selection being able to optimise male and female function in separate individuals to selection optimising male and female function together in the same individual.  Your research will illuminate the selective mechanisms – such as antagonistic selection – that are hypothesised to underpin the evolution of sex differences [6].

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) [3, 7], so, one of the strengths of your project is that you will use a comparative approach to investigate gene expression changes in multiple species.

Your research will build upon work that has shown sex is genetically determined [5], 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identified sex linked scaffolds in the three genomes (male, female and hermaphrodite) we have sequenced and assembled (unpublished).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 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 [8].   

Possible hypotheses to test:

Are genes with female biased expression in dioecious populations are less biased in hermaphrodites (and vice versa for male baised genes)?

Is there an effect of genome position (e.g. within or outside the sex chromosome region) of genes on the degree of change in expression bias?

Do independent evolutions of hermaphroditism show convergent patterns of expression change?

A male Triops cancriformis. Self -fertilising hermaphrodites have recently evolved from populations of outcrossing males and females. This represents an excellent model to understand the evolutionary genetics of sexual mode switching.

Methodology

You will rear Triops in the laboratory until adulthood 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.

You will assemble transcriptomes by alignment to already assembled genomes and perform differential expression analysis using appropriate bioinformatic programmes. You will analyse Gene Ontology of differentially expressed genes.

You will analyses gene expression change with respect to:

Sex specific region genes identified in silico from the annotated genome in conjunction with known sex-specific RAD markers [5].

Candidate genes involved in sex determination pathways in other invertebrates identified.

You will develop functional knockdowns of genes (e.g. RNAi) of differentially expressed genes and with known involvement in sex determination.

Training and Skills

CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes. 

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 recently supervised a NERC funded PhD student (Mark Harrison, currently a postdoc at University of Muenster, 1 paper, 3 in review) that used RNAseq [9], the primary research method used in this project.

 

Further Details

For further informal discussion please contact:

Dr Rob Hammond, Department of Genetics & Genome Biology, University of Leicester.

rh225@le.ac.uk

phone: 0116 252 5302