Figure 6.

Results from empirical datasets follow predictions from simulations

(A) PPA-Div and PPA-Mean scores for all three empirical datasets when the alignments are analyzed as amino acids and Dayhoff-6 recoded data. Average PPA scores for our simulated data are also reported (under nCAT10), indicating that PPA scores achieved for the simulated data under nCAT10 are comparable to those achieved under nCAT60 for the empirical datasets. (B) Support for Ctenophora-sister as different data types (amino acids, 0%-recodings, 90%-recodings, and Dayhoff-6) are used. (C) Support for Porifera-sister as different data types (amino acids, 0%-recodings, 90%-recodings, and Dayhoff-6) are used. In Orange: reference support values obtained for the two considered clades in our simulations. Light Green: Whelan2015; Dark Green Whelan2017; Blue Laumer2019. Note: Support values for 0%-recodings and 90%-recodings represent average values calculated over all random recoding generated.