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Phylogenetic applications of the minimum contradiction approach on continuous characters.

Thuillard M, Fraix-Burnet D - Evol. Bioinform. Online (2009)

Bottom Line: We explain how to discover the main structuring characters in a tree.The second set consists of a sample of 100 galaxies.In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.

View Article: PubMed Central - PubMed

Affiliation: La Colline, 2072 St-Blaise (Switzerland). thuillweb@hotmail.com

ABSTRACT
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa, the variables values can be embedded into a function with at most a local maximum and a local minimum, and crossing any horizontal line at most twice. In real applications, the order of the taxa best satisfying the above conditions can be obtained using the Minimum Contradiction method. This approach is applied to 2 sets of continuous characters. The first set corresponds to craniofacial landmarks in Hominids. The contradiction matrix is used to identify possible tree structures and some alternatives when they exist. We explain how to discover the main structuring characters in a tree. The second set consists of a sample of 100 galaxies. In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.

No MeSH data available.


A) Examples of independent characters, B) X-tree corresponding to the first two examples, C) The characters f1 and f2 are not independent.
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f6-ebo-2009-033: A) Examples of independent characters, B) X-tree corresponding to the first two examples, C) The characters f1 and f2 are not independent.

Mentions: Figure 6a shows 3 examples of independent characters. If two characters are independent and the taxa are perfectly ordered on both f1 and f2, then the distance matrix corresponds to a split network or an X-tree different from a line tree. Let us discuss the first example in Figure 6. Without restriction, let us assume that for the reference taxon n, f1(n) = f2(n) = 0. The distance matrix elements are given by


Phylogenetic applications of the minimum contradiction approach on continuous characters.

Thuillard M, Fraix-Burnet D - Evol. Bioinform. Online (2009)

A) Examples of independent characters, B) X-tree corresponding to the first two examples, C) The characters f1 and f2 are not independent.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2747132&req=5

f6-ebo-2009-033: A) Examples of independent characters, B) X-tree corresponding to the first two examples, C) The characters f1 and f2 are not independent.
Mentions: Figure 6a shows 3 examples of independent characters. If two characters are independent and the taxa are perfectly ordered on both f1 and f2, then the distance matrix corresponds to a split network or an X-tree different from a line tree. Let us discuss the first example in Figure 6. Without restriction, let us assume that for the reference taxon n, f1(n) = f2(n) = 0. The distance matrix elements are given by

Bottom Line: We explain how to discover the main structuring characters in a tree.The second set consists of a sample of 100 galaxies.In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.

View Article: PubMed Central - PubMed

Affiliation: La Colline, 2072 St-Blaise (Switzerland). thuillweb@hotmail.com

ABSTRACT
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa, the variables values can be embedded into a function with at most a local maximum and a local minimum, and crossing any horizontal line at most twice. In real applications, the order of the taxa best satisfying the above conditions can be obtained using the Minimum Contradiction method. This approach is applied to 2 sets of continuous characters. The first set corresponds to craniofacial landmarks in Hominids. The contradiction matrix is used to identify possible tree structures and some alternatives when they exist. We explain how to discover the main structuring characters in a tree. The second set consists of a sample of 100 galaxies. In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.

No MeSH data available.