Tooling up for the Tree of Life

University of Glasgow funded PhD studentship starting October 1, 2003

Division of Environmental and Evolutionary Biology
Institute of Biomedical and Life Sciences
University of Glasgow

Supervisors: Roderic Page (email: r.page@bio.gla.ac.uk) and Ela Hunt

The "Tree of Life" is one of the large-scale questions in biology -- what is the evolutionary history of all organisms on the planet? Comparable in magnitude to the human genome project, tackling this problem requires solving several computational and database problems. These include developing methods to assemble larger trees from smaller trees (the "supertree" problem), and developing tools to establish consistent taxonomic classifications.

As efforts to reconstruct the tree of life gain momentum, there is a growing need for phylogenetic databases to support this research. Amongst the most pressing needs are a curated taxonomy to ensure consistent naming of organisms in the database, and support for hierarchical queries using that taxonomy. There is also a need to store and query across large numbers (many thousands) of trees (e.g., find those trees with/without a specified relationship). Developing a phylogenetic database raises a number of issues about database design, querying trees and other graphs, and storing diverse kinds of data. This project will develop methodologies and tools to support phylogenetic databases. Test data will be provided by the related project on bird supertrees, and other sources. It would suit a biologically minded computer scientist, or computationally literate biologist. An interest in graph theory, algorithms, databases, and programming would be an advantage.

Related projects:

Bird supertree (PhD currently available)

Tree searcher (Honours project by Kenenth Jackson)

More information:

Page Lab

NSF Tree of Life workshop reports

NSF call for Tree of Life proposals

ITIS (list of taxonomic names)

TreeBase (a database of phylogenies, see also Mary Walsh's essays on TreeBASE)

BBC Radio 4 Today Programme item on taxonomy (6 Mb mpg downoad)


How to apply

The Ph.D. will commence on 1 October 2003. Applicants for this position should possess (or expect to obtain) at least an Upper Second Class Honours Degree in a relevant biological subject. The PhD is funded by the University of Glasgow which will pay tuition at the home student rate for students from the UK and EU member states, plus a stipend of £8500 p.a.

Applications (consisting of a letter describing why you are interested in, and well qualified for, this position, plus a full C.V. with names and addresses including e-mail if possible of two academic referees) should be sent as soon as possible to:

Dr Roderic D. M. Page
DEEB, IBLS
Graham Kerr Building
University of Glasgow,
Glasgow G12 8QQ
email: r.page@bio.gla.ac.uk


Lab environment

The supervisor (Rod Page) has a longstanding interest in consensus and supertrees. Algorithms developed have been incorporated into TreeBASE, which is a repository for phylogenetic databases and trees. We have already assembled a pilot data set of > 100 bird phylogenies for use in this project. Other projects underway in the lab include a phylogeny of vertebrates based on analysis of nuclear gene familes, and studies of seabird evolution and phylogeny, and seabird louse phylogeny and cospeciation. The Page lab is also home to TreeView, GeneTree, and other phylogenetic programs.


Glasgow

Glasgow University is set in the vibrant West end of Glasgow. The University of Glasgow visitors web site lists numerous links to life in Glasgow. The DEEB has a large and friendly graduate student population.