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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.


The tree associated to a single character is a line tree. In a line tree, all taxa are on the same path.
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f5-ebo-2009-033: The tree associated to a single character is a line tree. In a line tree, all taxa are on the same path.

Mentions: A central distinction can be made between the taxa depending on whether the character value is smaller or larger than the value of a reference taxon n. The set of taxa can be divided into two disjoint sets, the set S of taxa with values smaller or equal to the reference value f1(n) and the set of taxa L with values larger than the reference value (See Fig. 5 for an illustration). Let us show that a distance matrix fulfilling the conditions i) and ii) is perfectly ordered for any 3 ordered taxa i ≤ j ≤ k. We will consider all possible cases.


Phylogenetic applications of the minimum contradiction approach on continuous characters.

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

The tree associated to a single character is a line tree. In a line tree, all taxa are on the same path.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5-ebo-2009-033: The tree associated to a single character is a line tree. In a line tree, all taxa are on the same path.
Mentions: A central distinction can be made between the taxa depending on whether the character value is smaller or larger than the value of a reference taxon n. The set of taxa can be divided into two disjoint sets, the set S of taxa with values smaller or equal to the reference value f1(n) and the set of taxa L with values larger than the reference value (See Fig. 5 for an illustration). Let us show that a distance matrix fulfilling the conditions i) and ii) is perfectly ordered for any 3 ordered taxa i ≤ j ≤ k. We will consider all possible cases.

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.