My research interests are in organizing, interpreting, and interrogating data by creating novel software tools. So far I've used tools to test DNA barcoding across all of Diptera, and sub-Saharan biodiversity hotspots in robber flies. While working at lab, I created SequenceMatrix, an easy-to-use tool for assembling large datasets for phylogenetic analysis.
Studying biodiversity hotspots introduced me to the challenges and complexities of working with georeferenced specimen data, and I'd like to work further in this area. I'm particularly interested in the informatics of taxonomic information, the distribution of species and specimens in space and time, and in creating software tools which will make it easier to build up a comprehensive view of life on earth.
- Sequence Matrix
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Sequence Matrix is a visualization and editing program for large datasets. It uses a spreadsheet-like interface to simplify assembly of NEXUS or TNT datasets from a number of input formats. Assembled NEXUS or TNT files can also be resplit into their constituent files. Built-in tools help you analyse subsets of data or scan your dataset for suspicious pairwise distances, which may then be temporarily removed from your dataset before export. I wrote the software and presented it at a scientific conference.
- Sequence Matrix website
- My presentation on Sequence Matrix at the Hennig XXVIII conference in June 2009.
- Vaidya, G., Lohman, D. J., Meier, R. 2010 Sequencematrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics, accepted. Available online.
- Biodiversity hotspots
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Since 2003, my lab has been testing biodiversity hotspots for invertebrates using datasets on African (sub-Saharan) robber flies (insects of the Asilidae family) and peacock flies (insects of the Tephritidae family). We use "fake" hotspots to compare "true" biodiversity hotspots against in terms of species numbers and species endemism.
I performed the species estimate analyses in EstimateS during our first run at this project. In our second run, I created further "fake" hotspots across Africa in ArcGIS and wrote software tools in Perl to perform all the necessary data analysis quickly. Since I moved off this project in 2005, my tools have continued to be used, and have even been extended, by other undergraduate and graduate students to work on this project. In 2010, I've been asked to help out with an Honours project attempt to conclusively ending this project, currently in progress.
- Dikow, T., Meier, R., Vaidya, G.G. and Londt, J.G.H. 2009 Biodiversity research based on taxonomic revisions - a tale of unrealized opportunities. Diptera Diversity: Status, Challenges and Tools. (eds Pape, T., Bickel, D. and Meier, R.). Koninklijke Brill NV, Leiden. Available online.
- DNA barcoding
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In 2003, my lab began testing the feasibility of DNA barcoding by treating all the Diptera cytochrome oxidase unit I (cox1) sequences in NCBI GenBank as a DNA barcoding repository. I developed Species Identifier, a Java program which would treat every cox1 sequence as if it were from an unknown specimen, and try to identify it by comparing it against other sequences in the "repository". In this way, we studied how DNA barcoding would work in practice. We found that identification rates under these circumstances might be lower than 70%.
- Meier, R., Shiyang, K., Vaidya, G., Ng, P. K. 2006 DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55 (5), 715-728. Available online.
To find out more about my non-research achievements, please see my curriculum vitae.
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