Limits...
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.


Examples showing how characters supporting well a split can be identified using Prop. 1 in this article. The order is the same as in Table I. A) The character “Facial retraction: landmark 9” supports the split between Homo without H. habilis and H. rudolfensis and the other taxa. B) Split for the character “Facial retraction: landmark 9”.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f9-ebo-2009-033: Examples showing how characters supporting well a split can be identified using Prop. 1 in this article. The order is the same as in Table I. A) The character “Facial retraction: landmark 9” supports the split between Homo without H. habilis and H. rudolfensis and the other taxa. B) Split for the character “Facial retraction: landmark 9”.

Mentions: Contrarily to González-José et al our analysis is done without using a Principal Components Analysis (PCA). This simplifies considerably the interpretation of the results. Landmarks satisfying to a good approximation Prop. 1 can be identified quite simply. Once those characters are identified, one can discover which splits are supported by each character. Figure 9 shows a character that supports the second interpretation of Figure 8. The landmark 9 (Facial retraction) supports a split between Homo without H. habilis and H. rudolfensis and the other taxa. In that example, both interpretations are equally valid.22


Phylogenetic applications of the minimum contradiction approach on continuous characters.

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

Examples showing how characters supporting well a split can be identified using Prop. 1 in this article. The order is the same as in Table I. A) The character “Facial retraction: landmark 9” supports the split between Homo without H. habilis and H. rudolfensis and the other taxa. B) Split for the character “Facial retraction: landmark 9”.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f9-ebo-2009-033: Examples showing how characters supporting well a split can be identified using Prop. 1 in this article. The order is the same as in Table I. A) The character “Facial retraction: landmark 9” supports the split between Homo without H. habilis and H. rudolfensis and the other taxa. B) Split for the character “Facial retraction: landmark 9”.
Mentions: Contrarily to González-José et al our analysis is done without using a Principal Components Analysis (PCA). This simplifies considerably the interpretation of the results. Landmarks satisfying to a good approximation Prop. 1 can be identified quite simply. Once those characters are identified, one can discover which splits are supported by each character. Figure 9 shows a character that supports the second interpretation of Figure 8. The landmark 9 (Facial retraction) supports a split between Homo without H. habilis and H. rudolfensis and the other taxa. In that example, both interpretations are equally valid.22

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.