City Research Online

Abstract

The analysis of rooted trees is important in biology and many other fields of study. Despite this, tree shape as a whole is not fully exploited, and the insights it can provide and its limitations are poorly understood. Additionally, the indices that are currently used to quantify and describe tree shape have properties that complicate interpretation and limit their applications.

This thesis uses and evaluates a newly proposed system of indices designed to address these limitations. The indices account for branch lengths and type abundances as well as tree topology, are robust to small changes to the tree, are universally applicable, and have straightforward interpretations. Using this system, the thesis investigates tree shape and the insights it can provide in macroevolution and cancer settings.

The results demonstrate that tree shape can capture meaningful signals across a range of contexts, including branching rate heterogeneity, differences between modes of evolution and associations with disease-free survival in cancer trees. Although tree balance often performs well, it is not the only index that is informative, and reliance on balance alone can neglect important aspects of tree shape. Across the settings I considered, the system of indices used here frequently outperforms existing alternatives.

Taken together, this thesis strengthens the case for tree shape as a broadly applicable tool for studying evolutionary processes, and highlights the importance of using a system of indices that are also robust, universal, and interpretable to fully exploit the information captured by tree shape.

Publication Type:	Thesis (Doctoral)
Subjects:	Q Science > QA Mathematics Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics R Medicine > RC Internal medicine > RC0254 Neoplasms. Tumors. Oncology (including Cancer)
Departments:	School of Science & Technology > Department of Mathematics School of Science & Technology > School of Science & Technology Doctoral Theses Doctoral Theses

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