The excel document “SeedplantSimulationData.xls” contains the supplemental data for
the manuscript “Assessing Systematic Error in the Inference of Seed Plant Phylogeny” by
J. G. Burleigh and S. Mathews. It has the full results of the parametric bootstrap
analyses.
The first page in the excel document gives the full results for the parametric bootstrap of
the single locus data sets when the simulated data sets were analyzed using maximum
parsimony (MP). Each locus was analyzed using all sites, just the RC23 sites, and just
the RC4 sites. The tables are set up just like Table 1 in the manuscript. Five seed plant
hypotheses were examined: GP = gnepine; GF = gnetifer; AN = anthophyte; GS =
Gnetales sister to seed plants; GSG = Gnetales sister to gymnosperms. The columns with
the seed plant hypotheses listed on top represent the seed plant hypothesis that was
simulated; the rows represent the percentage of times each seed plant hypothesis was
recovered from the simulated data sets. The row “other” represents the percentage of
times a topology that is not consistent with any of the five listed seed plant hypotheses
was recovered. . “BS” is the nonparametric bootstrap score obtained from the empirical
data set. The bootstrap and adjusted bootstrap values from these analyses are listed in
table 2a.
The second page in the excel document gives the full results for the parametric bootstrap
of the single locus data sets when the simulated data sets were analyzed using maximum
likelihood (ML). Each locus was analyzed using all sites, just the RC23 sites, and just
the RC4 sites. Again, the tables are set up just like Table 1 in the manuscript. Five seed
plant hypotheses were examined: GP = gnepine; GF = gnetifer; AN = anthophyte; GS =
Gnetales sister to seed plants; GSG = Gnetales sister to gymnosperms. The columns with
the seed plant hypotheses listed on top represent the seed plant hypothesis that was
simulated; the rows represent the percentage of times each seed plant hypothesis was
recovered from the simulated data sets. The row “other” represents the percentage of
times a topology that is not consistent with any of the five listed seed plant hypotheses
was recovered. . “BS” is the nonparametric bootstrap score obtained from the empirical
data set. The bootstrap and adjusted bootstrap values from these analyses are listed in
table 2b.
The third page lists the results for the parametric bootstrap of the 12-locus data sets. All
the data from this page is found in Table 3 of the manuscript.