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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.


Minimum contradiction matrix Yi,jn on a set of 20 hominid taxa using Gorilla gorilla as reference taxon n.
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f8-ebo-2009-033: Minimum contradiction matrix Yi,jn on a set of 20 hominid taxa using Gorilla gorilla as reference taxon n.

Mentions: Similarly to González-José et al, we have preprocessed the 4 sets of landmarks with the Generalized Procrustes Analysis in Morphologika.20 The Generalized Procrustes analysis is a superimposition method that rotates, scales and translates the landmarks to adjust for isometric effects of size and orientation. The distance between two taxa is computed as the sum of the absolute difference between each Procrustes coordinate. The best circular order was subsequently obtained by minimizing the contradiction C in Eq. (1).11 Figure 8 shows the minimum contradiction matrix using Gorilla gorilla as reference taxon. Gorilla gorilla is taken as the reference taxon in order to be able to compare the results with González-José et al.


Phylogenetic applications of the minimum contradiction approach on continuous characters.

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

Minimum contradiction matrix Yi,jn on a set of 20 hominid taxa using Gorilla gorilla as reference taxon n.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f8-ebo-2009-033: Minimum contradiction matrix Yi,jn on a set of 20 hominid taxa using Gorilla gorilla as reference taxon n.
Mentions: Similarly to González-José et al, we have preprocessed the 4 sets of landmarks with the Generalized Procrustes Analysis in Morphologika.20 The Generalized Procrustes analysis is a superimposition method that rotates, scales and translates the landmarks to adjust for isometric effects of size and orientation. The distance between two taxa is computed as the sum of the absolute difference between each Procrustes coordinate. The best circular order was subsequently obtained by minimizing the contradiction C in Eq. (1).11 Figure 8 shows the minimum contradiction matrix using Gorilla gorilla as reference taxon. Gorilla gorilla is taken as the reference taxon in order to be able to compare the results with González-José et al.

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.