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Table 1 Number of events in parsimonious scenarios depending on PARS algorithm parameters

From: Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

Event

Number of genes (COGs)a

  

g = 1

g = 2

g = 3

  

General

independence

General

Independence

General

Independence

  

G

U

G

U

G

U

G

U

G

U

G

U

I

Number of genes in LUCA

572

315

506

305

956

788

926

750

1211

1049

1179

1029

II

Total gain

8661

11281

8892

11343

5812

6857

5853

6957

4461

5143

4476

5166

III

Horizontal transfer (II-3166) b

5495

8115

5726

8177

2646

3691

2687

3791

1295

1977

1310

2000

IV

Total loss

5121

2501

4909

2458

9944

7854

9953

7745

13695

11649

13736

11666

V

Total events (II + IV)

13782

13782

13801

13801

15756

14711

15806

14702

18156

16792

18212

16832

VI

Inconsistency score [g(II + IV)]

13782

13801

21568

21659

27078

27164

VII

Average number of scenarios per COG

2.10

1.74

1.36

1.27

1.23

1.18

VIII

Single-scenario COGs

1806

1944

2399

2518

2587

2666

IX

Maximum number of scenarios

39

18

8

7

8

6

  1. aall data are for the genome-tree topology; G stands for PARS-G algorithm and U for PARS-U algorithm bThe number of horizontal transfers was derived from the total gain number by subtracting the total number of COGs, 3166, because any COG must have emerged in one of the ancestral forms.