Tree figures

Figures of the phylogenetic trees produced in this study using Cox1 and 28S datasets. For each superfamily are represented the ML tree based on 28S dataset, and the PTP and GMYC trees produced using Cox1 datasets. Trees were built using Maximum Likelihood (ML) implementations using the GTR+GAMMA model of rate substitution (the most inclusive model) inferred using RAxML HPC2 (Stamatakis 2006) on Teragrid v.7.2.7, implemented in the Cyber Infrastructure for Phylogenetic Research (CIPRES) portal v.3.1. (Miller et al. 2011). One hundred independent searches, each starting from distinct random trees, were conducted. Robustness of the nodes was assessed using nonparametric bootstrapping (Felsenstein 1985) with 1000 replicates. For Cox1 datasets, the resulting tree served as input for the PTP model. For GMYC, the ML trees were made ultra-metric using r8s (Sanderson 2003). Trees were calibrated using divergence time and absolute rate of substitution between roots (fixed to have an arbitrary age of 1.0) and all unfixed nodes. Calibrations were reconstructed using the Langley-Fitch method and Powell’s algorithm (Sanderson 2003). PTP and GMYC analyses were both run using the ETE package (Huerta-Cepas et al. 2010).