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    Novel Mathematical Aspects of Phylogenetic Estimation (2009)

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    Type of Content
    Theses / Dissertations
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    http://hdl.handle.net/10092/2331
    http://dx.doi.org/10.26021/8354
    
    Thesis Discipline
    Mathematics
    Degree Name
    Doctor of Philosophy
    Publisher
    University of Canterbury. Mathematics and Statistics
    Collections
    • Engineering: Theses and Dissertations [2975]
    Authors
    Fischer, Mareike
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    Abstract

    In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. Inferring this underlying tree is challenging. We investigate some curious cases in which different methods like Maximum Parsimony, Maximum Likelihood and distance-based methods lead to different trees. Moreover, we state that in some cases, ancestral sequences can be more reliably reconstructed when some of the leaves of the tree are ignored - even if these leaves are close to the root. While all these findings show problems inherent to either the assumed model or the applied method, sometimes an inaccurate tree reconstruction is simply due to insufficient data. This is particularly problematic when a rapid divergence event occurred in the distant past. We analyze an idealized form of this problem and determine a tight lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). Finally, we investigate the problem of intermediates in the fossil record. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. We take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found.

    Keywords
    phylogenetics; maximum parsimony; maximum likelihood; fossils
    Rights
    Copyright Mareike Fischer
    https://canterbury.libguides.com/rights/theses

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