For each of our phylogenomic datasets, PhyloFisher scripts [119] were used for fast site removal, heterotacheous site removal, and random gene subsampling. The fastest evolving sites were sequentially removed in 6000 site chunks generating new alternative datasets at each step until all sites were removed (as in [31, 32]). Similarly, the most heterotacheous sites [33] were removed in a stepwise fashion, 6000 sites at a time, producing iteratively smaller datasets until no further sites could be removed. Genes from our 74 taxon datasets were randomly subsampled in sets of 20%, 40%, 60%, and 80% of the complete dataset, under the default 95% confidence interval setting as in Brown et al. [31]. The dataset comprised of genes unique to dataset A was similarly subjected to fast site removal, with 3000 sites being removed at each step. All datasets generated by these scripts were then subjected to phylogenetic analysis using IQtree under the LG+C60+F+G model with 100 non-parametric bootstrap replicates generated using PMSF and the fast setting in IQtree. In the case of fast evolving site removal under the LG model, 100 rapid bootstraps were generated using RAxML v8 (PROTCATLGF).

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