1. SUPPORT and RESAMPLING
Thanks to Leandro Gaetano

2. Support
Branch length
Bremmer support
Bootstrap
Jacknife

3. Bremer Support (decay index) (Bremer 1992) :
is the number of extra steps needed to "collapse" a branch
the absolute amount of favourable evidence supporting the group
Having a Bremer Support of 2 can have two meaning:
• A branch is supported by two uncontradicted characters. Therefore, it can only “cost” two steps not to have that branch.
• A branch is supported by n characters, but contradicted by n-2. Therefore, to prefer the contradictory branch “costs” only 2 steps.

4. Support

5. Support
Bremer support

6. Bremer Support Support BS= 2 BS= 1
There are some incongruences between characters. Bremer support will be the difference between the number of congruent characters (F) and the number of characters that contradict the branch

7. Bremer Support: Problems
If heuristic search is not complete and memory in insufficient (= hold low), the consensus for the suboptimal trees can be overresolved and the BS being artificially high
What BS is considered good?
solution?
As a rule of thumb, a Bremer score of 3 is good and a score of 5 suggests that the group is highly supported

8. relative Bremer Support (Goloboff and Farris, 2001)
Bremer relative = (F-C)/F
F = number of characters congruent with the branch
C = number of characters contradicting the branch
If relative Bremer support is 1 is totally supported if 0 not supported at all

9. Resampling
The bootstrap intention is to examine the relative
"confidence" associated with portions of a cladogram in relation to character sampling (Sidall, 2001).
Bootstrap
Resampling characters from the original data matrix, creating a pseudoreplicate matrix and then recalculating the most parsimonious tree on the pseudoreplicate
data.
From Soltis and Soltis (2003)

10. Stability can be defined only by reference to some factors (e. g
Stability can be defined only by reference to some factors (e.g., a group stable under addition of characters may be very unstable under addition of taxa or under recoding of some characters).
Support depends exclusively on presently available evidence (and, of course, assumptions or theories used to interpret that evidence).
Resampling evaluates support because the frequency with which replicates display a given group will be determined by the relative amounts of favourable and contradictory evidence

11. From Soltis and Soltis (2003)

12. Bootstrap: Problems Resampling
Boostrap not valid statistically for very large data-matrices
Unilateral support, meaning:
Recovered groups will be well supported
BUT might be not recovered groups that can have also good support
It is not clear what value of Boostrap is significant

13. Jackknife TAXONOMIC JACKKNIFE CHARACTER OR PARSIMONY JACKKNIFE
Resampling
What would have happened if I had fewer taxa or characters than I presently have, and then added the remainder?
Jackknife
TAXONOMIC JACKKNIFE
CHARACTER OR PARSIMONY JACKKNIFE

14. TAXONOMIC JACKKNIFE
Pseudoreplicas: remove one taxon from the data matrix and search for most parsimonious tree(s). This is repeated removing all the taxon from the matrix one every time (Pseudoreplica include all taxa -1)
2) Consensus from the trees obtained with all the pseudoreplicas
3) The Jackknife value represents the proportion of trees in which the groups recovered in the shortest tree(s) are represented

15. TAXONOMIC JACKKNIFE
From Sidall 2001

16. Bremer Support and Jackniffing can give different support values to monophyletic groups.
Compare values between monophyletic groups LM and FG.