SUPPORT and RESAMPLING Thanks to Leandro Gaetano

Support Branch length Bremmer support Bootstrap Jacknife

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.

Support

Support Bremer support

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

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

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

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)

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

From Soltis and Soltis (2003)

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

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

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

TAXONOMIC JACKKNIFE From Sidall 2001

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