Character fit and consensus Thanks to Leandro Gaetano.

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Presentation transcript:

Character fit and consensus Thanks to Leandro Gaetano

CHARACTER 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 Charci 11/1 = ½= 0,5 6 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)

CONSENSUS

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 ABCDEFGHIRepresentation 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 consensus Include groups that appears in the majority of the fundamental cladograms ABCDEFGHIRepresentation 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 ABCDEFGHIRepresentation 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 ABCDEFGHIRepresentation of the group  2  3  2  2  1  2  1  2  1  1  1  1  1