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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.