Institution: Cardiff University
Lead supervisor: Professor Michael Bruford
Wetlands are one of the most threatened ecosystems in Southern Africa, having suffered recent severe loses due to human landscape modification. Here we propose to study wetland connectivity using a phylogeographic approach with the Blacksmith lapwing, an endemic wetland bird to Southern Africa. We will analyse two gene sequences (ND2 and Cyt B) for populations sampled in Zimbabwe, South Africa, Mozambique and Botswana. To achieve this objective, a student will be trained in the molecular and statistical methods required by a current GW4+ student supervisor, Josephine Jackson. The undergraduate student will share lab and office space, enabling them to benefit from experiencing work in a molecular ecology lab where a wide variety of research questions including conservation, behaviour, food security, climate change and evolutionary processes are studied. General consumables and lab facilities are provided: additional required resources are requested here. The student will receive comprehensive training in molecular skills (DNA extraction, PCR amplification, gel electrophoresis). Followed by training and the completion of phylogeographic analysis. Samples are already collected and stored in Cardiff University. In addition to providing training in molecular and statistical skills, this student will be encouraged to take the lead in writing a report in manuscript style for possible publication, with support from the GW4+ student supervisor, so they will also receive training in scientific writing styles and publication preparation. There are no intellectual property issues. This is a novel and independent project with no previous data collected therefore there are no conflicts with the student’s previous or future work.
Indicative timescale of project (subject to change)
Molecular lab methods: DNA extraction, PCR amplification of two mitochondrial genes ND4 and CytB, gel electrophoresis
Bioinformatic work: analysis of raw sequences, creating phylogenetic trees and networks, population genetic statistics. Writing report
Week 1: DNA extraction training and extraction of 50 samples.
Week 2: PCR amplification and gel electrophoresis training
Week 3: PCR application for both genes
Week 4: Complete PCR amplification and prepare for sequencing
Week 5: statistical training for phylogenetic programs
Week 6: raw data analysis and start phylogenetic analysis
Week 7: continue phylogenetic analysis
Week 8: writing report in the form of a scientific paper.
Week 9: complete report and present the results of study during our weekly lab member meeting.