Figure 4.

ML tree with revised datasets N1, N9, and N10 (see also Figures S1, S9, and S10 in the Supplementary Material available online at http://dx.doi.org/10.1155/2016/1851865). PhyML (ver. 3.1) [51] was used for ML tree reconstruction using LG amino acid substitution model and four categories of evolutionary rates (Γ4). The tree search topology operations were based on the BEST option (both NNI and SPR algorithms). Bacterial, eukaryal, Lokiarchaeum (Loki 1), and the rest of the archaeal species are indicated in black, blue, purple, and red, respectively. The purple circle identifies the position of Loki 1. The scale bar represents the average number of substitutions per site. Values at nodes represent support calculated by nonparametric bootstrap (out of 100).