1. An Alternative Root for the Eukaryote Tree of Life
Ding He, Omar Fiz-Palacios, Cheng-Jie Fu, Johanna Fehling, Chun-Chieh Tsai, Sandra L. Baldauf 
Current Biology 
Volume 24, Issue 4, Pages (February 2014)
DOI: /j.cub
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2. Current Biology 2014 24, 465-470DOI: (10.1016/j.cub.2014.01.036)
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3. Figure 1
A Rooted Phylogeny of Eukaryotes Based on Thirty-Seven Eukaryotic Proteins of Bacterial Ancestry
The tree shown was derived from the full euBac data set (matrix M) by maximum likelihood using RAxML [8]. Branches are drawn to scale as indicated by the scale bar. Major groups are indicated by different colors and to the right with brackets and names. Nodal support from maximum-likelihood bootstrapping (mlBP, above branches) and Bayesian inference posterior probabilities (biPP, below branches) is shown only for nodes that did not receive full support (100% mlBP and 1.0 biPP). The inferred topologies from different data sets or analyses were identical except where indicated by dashed lines, for which only the highest support values are shown. Statistical support for the two nodes flanking the root (denoted a and b) is shown separately in the upper left for analyses with all alignment positions (matrix M), analyses with fast-evolving sites removed (matrix M′), or analyses with bacterial sequences masked for the ten euBac proteins with IOScore > 1.0 (matrix M″).
Current Biology  , DOI: ( /j.cub )
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4. Figure 2 Evolution of Phylogenetic Signal in the euBac Data Set
Matrices of increasing size (numbers of euBacs) were built by 500 rounds of random addition per matrix size class in increments of five (from 2 to 32) with the full euBac data set (A) and with bacterial sequences masked for the ten highest IOScore euBacs (IOScore > 1.0) (B). Three hypotheses for the eukaryote root were compared for each matrix in each size class using the approximately unbiased (AU) test [13] as follows: H1 (blue), Discoba sister to SA[R]P + Amorphea (neozoan-excavate root; Figure 1); H2 (red), Amorphea sister to Discoba + SA[R]P (unikont-bikont root; [1]); and H3 (green), SA[R]P sister to Amorphea + Discoba. Probabilities (boxplots) for the three hypotheses are plotted (y axis) against matrix size class (number of euBacs, x axis). The gray area at the bottom of each graph indicates rejection of the given hypothesis at p < Boxes were drawn from the first to the third quartile of the data, with median values indicated by the horizontal lines in the boxes. Dashed lines extending out of the boxes indicate the maximum and minimum values excluding the outliers.
Current Biology  , DOI: ( /j.cub )
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