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
2
3
2
2
1
2
1
2
1
1
1
1
1
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
2
3
2
2
1
2
1
2
1
1
1
1
1
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
2
3
2
2
1
2
1
2
1
1
1
1
1
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
2
3
2
2
1
2
1
2
1
1
1
1
1