After mapping a critical a posteriori evaluation of the character distribution using the parsimony principle was made, an approach well suitable for morphological phylogeny analyses [ 18, 24, 28, 74- 76] and described in detail in [ 74, 75].
The character state for the life history (tropical or temperate) was reconstructed on the total evidence consensus tree using parsimony character tracing (MacClade) [41].
To estimate the contribution of each dataset to the overall support of each node, partitioned Bremer support (PBS) values [ 46- 49] were calculated using TreeRot v.3 [ 50] and PAUP* using only the parsimony informative characters for each dataset and 1000 random addition replicates.
What is the effect of using the wrong character substitution model on the performance of a phylogeny reconstruction technique such as maximum parsimony?
To evaluate the variability of each locus, we calculated the number of characters that were constant, parsimony informative, and autapomorphic using the default parsimony settings in PAUP* [ 65].
The insertion/deletion matrix was analyzed using the maximum parsimony (MP) criterion in PAUP* as unordered characters with 10 random taxon additions and 200 bootstrap replicates.
Discrete character data were analyzed with PAUP v4.0, using maximum parsimony, with characters unweighted, character states unordered, with ACCTRAN character state optimization, treating multiple states as polymorphism, and running an exhaustive search.
To reconstruct the character evolution and groundplan features at each node, we used the "Trace Character History" option and performed maximum parsimony reconstructions of groundplans (select "Parsimony Ancestral States") for categorical characters under unordered states assumption.
Of all taxa placed via the evolutionary placement algorithm (EPA; Fig. 9), Osmunda pulchella is the species that is most incongruently placed between the different weighting schemes: Using parsimony-based character weights, the EPA places Osmunda pulchella at the root of Claytosmunda, whereas it is placed either between Osmundastrum and the remaining Osmunda s.str.str
Students were given instruction on mapping characters on alternative trees and choosing the most likely hypothesis of evolutionary relationships using the principle of parsimony (Smith and Cheruvelil, 2009).
