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 In Focus

Stories that DNA can tell

Published 2000-01-05

Professor Vincent Moulton, The Linnaeus Center for Bioinformatics, Uppsala University, MidSweden University on the Swedish side, and Professor David Penny of The Allan Wilson Center for Molecular Ecology and Evolution, Massey University and Dr Michael Steel, Department of Mathematics and Statistics, University of Canterbury started their STINT supported collaboration in the year 2000 within "Stories that DNA can tell". The project has received an annual funding of SEK 500 000.

Now that whole genomes are becoming available for many organisms, we have the unprecedented opportunity to uncover many of life’s secrets. In particular, by looking at molecular sequences that act as blueprints for organisms it is possible to understand how the organisms evolved. However, molecular data can be extremely complex, and it is necessary to develop mathematical models and computational strategies to uncover the stories hidden within genes, genomes and related data. The aim of this STINT project is precisely this.

The project brings together world-renowned scientists within disciplines such as mathematics, computer science, physics, bioinformatics, and biology at The Linnaeus Center for Bioinformatics (Uppsala University), MidSweden University, and The Allan Wilson Center for Molecular Ecology and Evolution (Massey University & University of Canterbury). It has been a resounding success, resulting in several exchanges between researchers and students at all levels, several joint papers appearing in diverse journals such as Molecular Biology and Evolution, Advances in Applied Mathematics, and Bioinformatics, and an international conference on Phylogenetic Combinatorics and Applications that will take place in Uppsala 2004.

Initial work focused on the continued development of new methods for constructing and analyzing evolutionary trees. Such trees represent the history of species, much in the same way as a family tree represents the relationships between past and present members of a family. This work has led to an active mathematical investigation of combinatorial and topological properties of phylogenetic trees and collections of trees or tree-space. Our research has provided ways to overcome limitations of current techniques for constructing evolutionary trees, and led to new ways to build supertrees, that is, trees displaying the information contained within collections of trees. These new methods will provide tools necessary for addressing the challenge of constructing the Tree of life.

In related work, new methodologies and computer programs have been developed for constructing phylogenetic networks. These mathematical structures can be used to analyze evolutionary histories that are not treelike, that can arise when studying organisms such as viruses and plants, which can share genetic information in biological processes such as recombination and hybridization. This has resulted in a highly active collaboration, and new techniques are being developed to better understand dispersal and radiation of New Zealand flora. In an exciting new direction, network methodology is being developed to provide new tools for studying plant biodiversity.

The project has also focused on the development of computational techniques for analysis of whole-genomes. For example, techniques have been jointly developed for discovering new RNA genes, genes that do not need to be translated to function in the cell, These and related results are being used to understand evolutionary problems such as the origins of life and the demise of the dinosaurs. In another direction, methods are being developed for constructing whole-genome phylogenies. This involves combining and interpreting the (sometimes contradictory) information locked within several genes.

The project has led to mathematical and computational tools for analyzing molecular evolution. As well as providing a strong foundation for understanding the fundamental biological mechanisms involved in evolution, it has strengthened an exciting collaboration between scientists in Sweden and New Zealand.

Vincent Moulton
Uppsala university

Senast uppdaterad: 04-10-18 10:32

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