Reweaving the tapestry--a supertree of birds

NERC funded PhD studentship starting October 1, 2003

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

Supervisor: Roderic Page (email: r.page@bio.gla.ac.uk

Birds play a prominent role in comparative studies of ecology, behaviour and evolution. Despite this, we still do not have a widely accepted phylogeny of the group. Many comparative studies default to using Sibley and AhlquistÕs now aging "tapestry," which is based on limited (and in places dubious) data. Some recent studies based on whole mitochondrial genomes have produced apparently absurd trees that have passerines (songbirds) at the base of the bird tree. Given this uncertainty and confusion, there are several ways to proceed. One is to try and obtain comparable data from a range of taxa, for example by sequencing the same gene in many bird orders. Several research groups are pursing this method. However, this approach effectively discards any data collected from other sources such as DNA hybridisation, allozymes, morphology, and behaviour. It also presupposes that a single gene (or suite of genes) will be able to address all levels of bird phylogeny. An alternative approach is to combine trees for different taxa and data sets into a single, all embracing "supertree."

This project will aim to reweave the tapestry by assembling a supertree for birds from all existing, published phylogenies. The student will do a literature and database search to locate avian phylogenies, and will then assemble them into a larger tree. We have successfully tried this method on petrels and albatrosses (Kennedy and Page, 2002) using software developed at Glasgow (RadCon). New methods for computing supertrees have been developed since Kennedy and Page, so as part of the project the student will compare different methods for constructing supertrees, and compare these supertree with results based on sequencing-only studies (supertrees can use sequence trees as well as other sources of data). In addition to evaluating the methodology, the project will generate the first large-scale bird phylogeny since the Sibley and Ahlquist.

This proposed research is very timely because of the growing interest in assembling the tree of all living things. The bird supertree project will enable us to assess how feasible the supertree approach is on a large, but manageable group. The results will be of broad interets to the systematics community, and to comparative biologists in general.

Related PhD project:

Tooling up for the Tree of Life

More information:

Page Lab

Tree of Life workshop reports

NSF call for Tree of Life proposals

Supertree server

Supertree bibliography

Kennedy, M. & Page, R.D.M. (2002). Seabird supertrees: Combining partial estimates of procellariiform phylogeny. The Auk, 119: 88-108. [PDF]


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, and should be eligible for a NERC studentship (please note that only UK citizens are eligible for full funding: other EU nationals are eligible only for payment of fees).

A background or interest in computer programming (especially C++ and/or Java), algorithms, and phylogenetics would be an advantage.

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.