The Mediterranean basin is a global hotspot for plant diversity. Three different plant groups are being studied using next generation DNA sequencing to understand impacts of climate change on the rate and tempo of speciation. UROP students will integrate with the PhD group to learn the science behind this research.
Department: Ecology and Evolutionary Biology
Supervised by: Alastair Culham
The Mediterranean basin is one of the world’s biodiversity hotspots yet patterns of distribution and diversification of species that are key to maintaining this biodiversity are still poorly understood. The steady rise in population and urban development makes the area at particular risk of biodiversity loss. This project aims to develop a model system for the study and understanding of Mediterranean plant species in relation to geological and climatic history through the Cenozoic using Narcissus (daffodils), Hyacinthineae and Cyclamen as an exemplar system. Recent meta-analyses (Escudero et al. 2017; Vargas et al. 2018) indicate Mediterranean species diversification may have started in the mid Cenozoic, before the formation of the Mediterranean climate zone. This project will develop time-calibrated phylogenetic trees for the exemplar plant groups. Previous work by Yesson & Culham on Cyclamen, in the Eastern Mediterranean suggested a range of physical factors including orogeny and climate influenced speciation that will be explored further in this project. The genetic patterns we are currently finding suggest there has been disruption to the distribution of these plants over varying geological timescales resulting in previously unreported genetic disjunctions. The generation of large data sets using next generation DNA sequencing will allow robust phylogenetic trees to be built. This is a time intensive process and these UROP students will work alongside three PhD students to help generate new sequence data and process data already generated.
The students will undertake: plant DNA extraction and quality assessment, preparation of samples for next generation DNA sequencing NGS), processing raw read data from NGS, assembling genes and genomes, quality control of data and sample management, processing of data for phylogenetic analysis and learning to Interpret phylogenetic output.
Basic knowledge of laboratory skills, Ideally Including pipette handling, basic chemistry knowledge to enable the understanding of DNA handling protocols, good record keeping skills, good teamwork skills.
The students will develop research level skills In DNA extraction from a range of species using both kit based and CTAB methods, preparing and handling gels for DNA quality testing, advanced DNA data handling skills and data analysis skills. Experience of drafting a scientific manuscript (writing skills and thinking skills) of high relevance to conducting a part 3 research project.
Health and Life Sciences Building, University of Reading Herbarium.
09.00-17.30
Wednesday 01 June 2022 - Wednesday 13 July 2022
The post will be advertised centrally on the UROP website between 21st February and 4th April 2022. Students should submit their CV and Cover Letter directly to the Project Supervisor (click on supervisor name at the top of the page for email). Successful candidates will be invited for an interview.