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In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the… (More)

Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods such as Maximum Parsimony need to be modified in order to be applicable to networks. In this paper, we discuss two… (More)

- Mareike Fischer
- 2012

In a recent study, Steel and Sanderson defined and characterized phylogenetically decisive sets of taxon sets. A set is called phylogenetically decisive if regardless of the trees chosen for each of its taxon sets, as long as these trees are compatible with one another, their supertree is always unique. This implies that the sampled taxon sets always lead… (More)

In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary relationship accurately depends on the model of sequence evolution, the substitution rate, divergence times and the method… (More)

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under consideration, and the goal is to find the… (More)

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under… (More)

Tuffley and Steel (Bull. Math. Biol. 59:581-607, 1997) proved that maximum likelihood and maximum parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been widely cited ever since. We show that small changes to the model assumptions suffice to… (More)

Given two phylogenetic trees on the same set of taxa X, the maximum parsimony distance dMP is defined as the maximum, ranging over all characters on X, of the absolute difference in parsimony score induced by on the two trees. In this note we prove that for binary trees there exists a character achieving this maximum that is convex on one of the trees (i.e.… (More)

The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequenc-ing is still a time-consuming and costly process. Therefore, decision criteria would be desirable to decide a priori which data might contribute new… (More)

In this paper, we investigate a conjecture by Arndt von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a… (More)