Character fit and consensus

Thanks to Leandro Gaetano

CHARACTER FITCHARACTER FIT

Character fit

• Consistence Index (Ci)

• Retention Index (Ri)

How well the data fit the tree(s)?

• Length (L)

Length

Consistency Index (ci); relative amount of homoplasy

ci = m / s

s = number of steps in the tree and m = character states-1

Char ci

1 1/1 = 1

2 1/1 = 1

3 1/1 = 1

4 1/1 = 1

5 ½= 0,5

6 ½= 0,5

Character fit

ci varies between 1 (no homoplasy) to values close to 0 (higher quantity of homoplasy)

Consistency Index

For the tree it is called ensemble consistency index; CI

Ajuste de caracteres

Consistency Index (ci): Problems

• Uninformative characters increment artificially the ci

• Negatively correlated with number of characters and of taxa. Not useful to compare trees with different number of terminals and characters

Retention Index (ri) ri= (g-s)/(g-m)

s= number of steps in the tree; m= number of states – 1; g= maximum number of steps that a character can have in the cladogram (number of taxa with state 0 or 1 , whichever is the lower

ri(3)= (3-1)/3-1)= 1

ri(6)= (2-2)/(2-1) = 0

Character fit

This is for individual characters

For the tree it is called ensemble retention index; RI

ri varies from 1 (no homoplasy) to 0 (higher quantity of homoplasy)

CONSENSUSCONSENSUS

Consensus

Consensus tree is used to explore congruence or

incongruence among the most parsimonious trees (also called

fundamental trees) of a cladistic analysis

Consensus

• Synthesis of information of most parsimonious trees

• Comparing different partitions of data

• For the calculation of branch support

When is consensus tree neccesary?

Consensus trees

Compromise cladograms

Take into account fundamental trees

Strict consensus Semistrict, of majority and of Adam consensus

Consensus

Strict consensus

A B C D E F G H I Representation of the group

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Show groups obtained in all the fundamental cladograms. Lack of resolution is represented as polytomy

Consensus

Majority consensusInclude groups that appears in the majority of the fundamental cladograms

A B C D E F G H I Representation of the group

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Consensus

Semiestrict consensus

Group represented in all the fundamental cladograms and groups no contradicted by any of these trees

A B C D E F G H I Representation of the group

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Consensus

Consenso

Conflictive taxa are relocated in a node common to all conflictive positions. Conflictive taxa remains separated by a polytomy

Adam consensus

A B C D E F G H I Representation of the group

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