The QMEE CDT Project proposal database

Welcome to the QMEE CDT Project proposal database. This is a live list of projects proposals put forward by PIs across the CDT partner institutions

PIs/Supervisors will continue to add projects to this list over the next few months, so do keep checking back! You can search the projects using the box below: simply enter some text and press Search to do a text search across all the database fields. If you want to search more finely, the search tool also allows you to search on particular details of the project descriptions: you will see these finer search options appear if you click on the search box.

Click on the view button next to a project to get the full proposal description. If you want to download project details, either for all projects, or for a subset you have searched for, then click on the 'Download details' button.

To find a particular PI's email or look up other PI details, use the menu at the top of this page (PIs tab).

Genome evolution in seahorses and their relatives: hormone signalling and sensitivity
Male pregnancy in seahorses is a unique vertebrate adaptation involving a suite of morphological, physiological and behavioural features. It is an extreme example of the more general phenomenon of paternal care in fish, where care of the young is largely by males. Seahorse male pregnancy has co-opted several of the same hormone pathways that regulate pregnancy and reproductive behaviour in mammals, such as progesterone and glucocorticoids, as well as possibly steroids novel to male pregnancy. This group is therefore a promising but underexplored model for hormone pathway evolution. Estaurine fishes are valuable sentinels to understand the role of endocrine disrupters (EDCs) that can disrupt both reproduction and sex-typical behaviours. Though most work on hormone biology in fish has been done on model species such as zebrafish and medaka, their year-round breeding may make them less sensitive in their response both to endogenous hormones and hormone-mimicking pollutants. This project aims to examine genome evolution, with special reference to the evolution of hormone signalling pathways, in seahorses and their relatives, by bioinformatic and phylogenetic methods. Genome sequences are currently available for two seahorse species, and several close relatives (pipefish, sea moth, dragonfish). In addition, pouch transcriptomes have been sequenced for the striped seahorse. Phylogenetic resources include a tree of 300 ray-finned fish taxa. The project includes some lower-risk components to build skills and confidence, and higher-risk components providing challenge and extra reward. The student will test for phylogenetic correlations between aspects of breeding system (seasonality, parental care) and sensitivity to hormone disruptors. (S)he will also test for heterogeneity of evolutionary rates both in breeding system and sensitivity phenotypes, and in a suite of relevant genes: those involved in hormone synthesis and response; those with high transcription rates in the brood pouch; those implicated in pollution sensitivity in laboratory studies. Shifts in the rate of molecular evolution may be expected in that conservation of sequence will be highest where there is most sensitivity to fluctuations in function. This approach may prove very useful in predicting which species will be most adversely affected by endocrine disruptors for example. We can also assess sex determination systems in species where this is not known, by categorising scaffolds by mutation rate, using male-biased mutation rates between species (male biased mutation is seen in the majority of animal lineages including many fish lineages) and transposable element densities to assign scaffolds to chromosome categories. Colleagues in Reading bring additional expertise in the interpretation of large-scale evolutionary patterns and phylogenetic analysis (Pagel, Venditti, Baker), life history evolution (Sibly), ecotoxicology (Callaghan) and conservation biology (Gonzalez-Suarez), as well as endocrinology (Knight, Bicknell). We have suitable expertise and facilities to be able to extend the results obtained to behavioural analyses and laboratory tests of our predictions. CEFAS is a world leader in marine science and technology specialising in translating expert knowledge into practical and innovative solutions for aquatic environments.
Louise Johnson
Ioanna Katsiadaki
Andrew Meade, University of Reading; Nandini Vasudevan, University of Reading
Computing, Quantitative data analysis
Andrew Meade
The student will be using and developing methods in computational phylogenetics, incorporating the analysis of molecular evolution inferred from large genome datasets, and developing statistical models of evolutionary processes.
This project is innovative in that it applies computational phylogenetics in new ways to new research areas and datasets and aims to develop methods beyond those currently available. We will be developing new methods of genome analysis with the sex chromosome prediction part of the project (small pilot studies on bird W/Z chromosomes have suggested this is a promising approach).
This is a genome evolution project incorporating ecology as a driver of genome evolution - ecology and evolution are not merely an element of the project but central to both the rationale and methodology.
The project has potential for real-world applications in informing us firstly in general how much caution is needed in applying laboratory-inferred sensitivity estimates for endocrine disrupting pollutants; and secondly in possibly allowing us to predict EDC sensitivity from phylogenetic relationships and (in the longer term) from genetic data.
Sequence data is increasingly fast and cheap to obtain, and thanks to megaprojects such as Earth Biogenomes, there will be an increasing number of species for which we have extensive genomic data but few field observations or natural history studies. Techniques developed in this project work towards predicting aspects of a species' natural history and response to environment from sequence data.
Disciplines represented include aquatic ecology and evolution; endocrinology and eco-toxicology; evolutionary genetics and genomics; biomedical science; computational phylogenetics and statistics.
Population genetics and evolution, Marine environments, Ecological/Evolutionary tools, technology & methods
Training will be provided in computational phylogenetics and evolutionary genetics, and the student will also participate in the lab meetings of the Vasudevan molecular endocrinology laboratory to enhance cross-disciplinarity.
University of Reading
2019-05-20 16:53:14