Fine-scale phylogeny using a mathematical model of the dynamics of rDNA repeat sequence evolution

自从查尔斯·达尔文提出他的进化论以来，生物学家们一直对重建生命树感兴趣，生命树代表了所有现代物种的进化史(http://www.phylo.org/).这是一个极其雄心勃勃的目标，因此生物学家通常专注于为现代物种的小亚群构建进化树。在过去，这种树的建造是基于物种的特殊特征，例如它们的骨骼或解剖结构的特性。然而，现在我们已经能够对部分基因组或在某些情况下对整个基因组进行排序，生物学家使用DNA数据构建进化树现在是司空见惯的事情。因此，近些年来，围绕着建造这样的树，出现了一种全新的理论，称为“系统遗传学”。在系统发育学中使用的最重要的DNA序列是核糖体DNA重复单位(或rDNA)，这是一段存在于所有物种中的DNA，已被用来构建“通用的”生命树。由于最近的大规模基因组测序项目，揭示了许多生物的DNA密码，包括非常密切的相关生物，如各种酵母菌株(或亚种)，我们现在有数据可用来构建更详细的系统发育图。特别是一些DNA序列，比如我们计划在这个项目中使用的rDNA序列，在基因组内和基因组之间都是不同的。这些DNA序列将使我们能够比以前更清楚地揭示密切相关的生物之间的关系，例如我们的酵母菌株。然而，将需要新的工具来执行所涉及的分析过程。计算生物学的最新进展意味着我们现在有能力建立快速有效的工具来实现这一目标。这个项目的目的是建立一种新的数学工具，在最基本的水平上分析rDNA序列的变异和动态。该工具将被应用于酵母数据，如果可能的话，还将用于植物数据，从而能够构建比迄今可能的更详细的系统发育图。酵母基因组为理解植物和包括人类在内的其他真核基因组的基因组动力学提供了极好的模型。因此，我们的新工具也可以被科学家使用，他们希望分析其他物种群体的数据集。

Ever since Charles Darwin introduced his theory for evolution, biologists have been interested in reconstructing the Tree of Life, the tree representing the evolutionary history of all present-day species (http://www.phylo.org/). This is an extremely ambitious goal, and so biologists usually concentrate on constructing evolutionary trees for small sub-collections of present-day species. In the past, the construction of such trees was based on particular characteristics of the species, such as properties of their skeleton or anatomy. However, now that we are able to sequence parts of genomes, or in some cases whole genomes, it is now commonplace for biologists to construct evolutionary trees using DNA data. Consequently, in recent years a whole new theory, called 'Phylogenetics', has grown around building such trees. The most important DNA sequence used in phylogenetics is that of the ribosomal DNA repeat unit (or rDNA), a section of DNA which is present in all species, and which has been used to construct the 'universal' tree-of-life. Thanks to recent large-scale genome sequencing projects, which have revealed the DNA codes of many organisms, including very closely related ones such as various yeast strains (or sub-species), we now have data available to construct far more detailed phylogenies. In particular some DNA sequences, such the rDNA sequences that we plan to use in this project, vary within genomes and well as between them. These DNA sequences will enable us to uncover the relationships between closely related organisms, such as our yeast strains, much more clearly than we have been able to do before now. However, new tools will be required to carry out the analytical processes involved. Recent advances in computational biology mean we now have the ability to build rapid and efficient tools to achieve this goal. The aim of this project is to build a new mathematical tool to analyse rDNA sequence variation and dynamics at the most basic level. The tool will be applied to yeast and, if possible, plant data, allowing much more detailed phylogenies to be constructed than hitherto possible. Yeast genomes provide excellent models for understanding genome dynamics in plants and in other eukaryotic genomes, including humans. Therefore, our new tool can also be used by scientists who wish to analyse datsets of other species groups.