On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa

Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was introduced by Semple et al in 2004. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence of embeddings into a common supertree, and of the joint properties of their cluster representations. Our analysis leads to a very simple polynomial-time algorithm for testing this compatibility, which we have implemented and is freely available for download from the BioPerl collection of Perl modules for computational biology.Comment: Submitte

Supertree algorithms for ancestral divergence dates and nested taxa

Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the `Tree of Life'. However, a limitation of such methods is that, typically, they use just leaf-labelled phylogenetic trees to infer the resulting supertree

Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics

Abstract. Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the `Tree of Life'. However, a limitation of such methods is that, typically, they use just leaf-labelled phylogenetic trees to infer the resulting supertree. Results: In this paper, we describe several new supertree algorithms that extend the allowable information that can be used for phylogenetic inference. These algorithms have been recently implemented and we describe here two illustrative applications. Availability: These new algorithms are freely available for application at http://darwin.zoology.gla.ac.uk/cgi-bin/build.pl Contact: [email protected] 1 Introduction Rooted phylogenetic trees are used in evolutionary biology to represent the an-cestral history of a collection of present-day species. For example, ignoring the numerals, Fig. 1 shows a rooted phylogenetic tree where the labels a, b, c, d, e,and f represent the present-day species. A supertree is a rooted phylogenetic treethat is the result of combining a collection of smaller rooted phylogenetic tree

Evolution of Tandemly Repeated Sequences

Despite being found in all presently sequenced genomes, the evolution of tandemly repeated sequences has only just begun to be understood. We can represent the duplication history of tandemly repeated sequences with duplication trees. Most phylogenetic techniques need to be modified to be used on duplication trees. Due to gene loss, it is not always possible to reconstruct the duplication history of a tandemly repeated sequence. This thesis addresses this problem by providing a polynomial-time locally optimal algorithm to reconstruct the duplication history of a tandemly repeated sequence in the presence of gene loss. Supertree methods cannot be directly applied to duplication trees. A polynomial-time algorithm that takes a forest of ordered phylogenies and looks for a super duplication tree is presented. If such a super duplication tree is found then the algorithm constructs the super duplication tree. However, the algorithm does not always find a super duplication tree when one exists. The SPR topological rearrangement in its current form cannot be used on duplication trees. The necessary modifications are made to an agreement forest so that the SPR operation can be used on duplication trees. This operation is called the duplication rooted subtree prune and regraft operation (DrSPR). The size of the DrSPR neighbourhood is calculated for simple duplication trees and the tree shapes that maximize and minimize this are given