Additional File 1:

Trees from truncated matrix with Acorus. These first- and second-position trees show that the results are essentially the same when positions that have Acorus data missing are removed. The first row using the ML HKY85 model is with four rate categories and parameters estimated as described in Methods. The third row uses the ML model parameters calculated as in the first row to calculate a distance matrix that was used for NJ analyses. For comparison the corresponding bootstrap values for Amborella sister to the angiosperms in the full matrix, going across each row, are 1. (99 vs. 100, 100 vs. 100), 2. (NA but same topology and similar BS, 100 vs. 100), 3. (86 vs. 88, 84 vs. 90).

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Additional File 2:

Trees from truncated RY-coded matrix with Acorus included. This are the same analyses as in Additional file 1 except the DNA is RY-coded. For comparison, the corresponding BS values for the Amborella sister relationship in the full matrix, along each row, are: 1. (100 vs. 100, 100 vs. 100), 2 (98 vs. 100, 100 vs. 100), 3. (100 vs. 100, 100 vs. 100).

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Additional File 3:

Comparison of gamma-distributed rates with two versus four rate categories. This figure shows that using two rate categories gives essentially the same results as using four rate categories with this dataset. The dataset is the first- and second-position, 61-gene matrix with grasses, Acorus, or both used to represent monocots. The ML HKY85 model was used and parameters were estimated as described in Methods.

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Additional File 4:

Trees when constant sites are removed from the first- and second-position matrix of Goremykin et al. [19]. A. ML HKY85 and equal rates. B. NJ with distances calculated using an ML HKY85 model and equal rates.

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Additional File 5:

NJ analysis using ML proportion of invariant distances. Distances were calculated using the ML HKY85 model, the estimated proportion of invariant sites, and the first- and second-position matrix of Goremykin et al. [19].

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Additional File 6:

ML trees using third positions only. A. HKY85 model with equal rates. B. HKY85 model with four gamma-distributed rates.

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Additional File 7:

Sister group to the rest of angiosperms found in individual gene analyses using first- and second-position data without Acorus Top, ML HKY85 with four gamma-distributed rates. Bottom, Parsimony analysis.

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Additional File 8:

Sister group to the rest of angiosperms found in individual gene analyses using the ML HKY85 model with four gamma-distributed rates and Acorus added. Top, all three positions. Bottom, first and second positions.

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Additional File 9:

Sister group to the rest of angiosperms found in individual gene analyses using the ML HKY85 model with four gamma-distributed rates with Acorus added and grasses removed. Top, all three positions. Bottom, first and second positions.

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Additional File 10:

Sister group to the rest of angiosperms found in individual gene analyses using parsimony on all three positions. Top, Acorus added. Bottom, Acorus added and grasses excluded.

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