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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 distance matrix Yi,jn (Fig. 7c) corresponding to two dependent characters f1(i) and f2(i) (Fig. 7a,b). The distance matrix corresponds to a split network (Fig. 7d). The split network is obtained with Splits Tree.16 The contradiction on the order of the taxa is zero (C = 0 in Eq. 2)
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f7-ebo-2009-033: The distance matrix Yi,jn (Fig. 7c) corresponding to two dependent characters f1(i) and f2(i) (Fig. 7a,b). The distance matrix corresponds to a split network (Fig. 7d). The split network is obtained with Splits Tree.16 The contradiction on the order of the taxa is zero (C = 0 in Eq. 2)

Mentions: Figure 7 is another illustration of Proposition 3 for two characters on perfectly ordered taxa. The ordered matrix Yi,jn = Yi,jn(f1) + Yi,jn(f2) is perfectly ordered. In this example, the distance matrix is described by a split network and not by an X-tree (A tree is a special case among split networks).10


Phylogenetic applications of the minimum contradiction approach on continuous characters.

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

The distance matrix Yi,jn (Fig. 7c) corresponding to two dependent characters f1(i) and f2(i) (Fig. 7a,b). The distance matrix corresponds to a split network (Fig. 7d). The split network is obtained with Splits Tree.16 The contradiction on the order of the taxa is zero (C = 0 in Eq. 2)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f7-ebo-2009-033: The distance matrix Yi,jn (Fig. 7c) corresponding to two dependent characters f1(i) and f2(i) (Fig. 7a,b). The distance matrix corresponds to a split network (Fig. 7d). The split network is obtained with Splits Tree.16 The contradiction on the order of the taxa is zero (C = 0 in Eq. 2)
Mentions: Figure 7 is another illustration of Proposition 3 for two characters on perfectly ordered taxa. The ordered matrix Yi,jn = Yi,jn(f1) + Yi,jn(f2) is perfectly ordered. In this example, the distance matrix is described by a split network and not by an X-tree (A tree is a special case among split networks).10

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.