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Table 1 Results of analyses for the control mitochondrial genome quartets #m1-m7.

From: Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

# Genome 1 Genome 2 Genome 3 Genome 4 ((1,2),3,4)   ((1,3),2,4)   ((1,4),2,3)
      Tot. A B   Tot. A B   Tot. A B
m1 Drosophila Drosophila Ceratitis capitata Apis mellifera 9 8 8   0 0 0   1 0 0
  melanogaster yakuba   ligustica 10 8 8   0 0 0   0 0 0
      9 7 5   0 0 0   1 1 0
m2 Alligator Opossum Stork Donkey 0 0 0   11 11 11   0 0 0
      0 0 0   11 11 11   0 0 0
      0 0 0   11 11 11   0 0 0
m3 Turtle Opossum Stork Donkey 0 0 0   12 12 12   0 0 0
      0 0 0   12 12 12   0 0 0
      0 0 0   12 12 12   0 0 0
m4 Starfish Donkey Fruit Fly Doorsnail 8 7 7   2 1 1   0 0 0
      8 7 7   1 0 0   1 0 0
      8 7 5   1 1 0   1 0 0
m6 Reclinomonas Saccharomyces Arabidopsis Homo sapiens 0 0 0   4 3 3   0 0 0
  americana cerevisiae thaliana   1 0 0   3 3 3   0 0 0
      0 0 0   4 3 2   0 0 0
m7 Cafeteria Saccharomyces Arabidopsis Homo sapiens 0 0 0   3 2 2   1 1 1
  roenbergensis cerevisiae thaliana   1 0 0   2 2 1   1 1 1
      1 0 0   2 1 0   1 1 1
  1. The groupings corresponding to the expected organismal phylogenies are given in bold. The three numbers in each table cell correspond to the three approaches used. The top number corresponds to results obtained using Strimmer and von Haeseler's approach [24], the middle number corresponds to results obtained using MrBayes program [31], and the bottom number corresponds to results of bootstrap support values calculation. Column "Tot." lists the number of QuartOPs from "total" zone, column A lists the number of QuartOPs from "90%" zone (70% for bootstrap support), and column B lists the number of QuartOPs from "99%" zone (90% for bootstrap support). For definition of zones see Fig. 2. With the exception of the one dataset for quartet #m7, the analyses proved to be consistent with organismal tree topologies. The alignment for the exceptional dataset is presented in Fig. 6. The common names for the organisms listed correspond to the following scientific names: alligator corresponds to Alligator mississippiensis, opossum to Didelphis virginiana, stork to Ciconia ciconia, donkey to Equus asinus, turtle to Chelonia mydas, starfish to Asterina pectinifera, doorsnail to Albinaria caerulia, fruit fly to Drosophila melanogaster.