Table 1 A list of Embryophyte gene families with high Ka/Ks values detected using whole gene averaging is shown. The p- value and expected rate of false positive detection given multiple tests per detected branch hypothesis (Bon*) are shown as a measure of statistical significance. Statistical significance is measured against simulated proteins evolved according to measured parameters rather than against evolved pseudogenes evolving neutrally at the amino acid level (as is sometimes used as a null model in evolutionary studies). The null distribution is therefore centered at 0.21 rather than 1.0.

136

Self incompatibility protein/S8-RNase

70

0.09

0.07

1.18 ± 0.02

<10e - 4

<0.5

0.07

0.07

1.04 ± 0.01

<10e - 4

<0.5

0.07

0.06

1.20 ± 0.02

<10e - 4

<0.5

0.09

0.08

1.10 ± 0.05

<10e - 4

<0.5

172

chitinase III

60

0.15

0.14

1.08 ± 0.01

<10e - 4

<1

218

Cystein proteinase IV

106

0.16

0.15

1.05 ± 0.01

<10e - 4

1

266

Xet2

58

0.10

0.10

1.02 ± 0.01

<10e - 4

<1

401

phytochrome A

637

0.06

0.05

1.12 ± 0.01

<10e - 4

<0.5

667

flowerspecific gamma thionin

7

0.17

0.13

1.29 ± 0.03

<10e - 4

<0.5

678

Metallocarboxypeptidase inhibitor

3

0.09

0.08

1.12 ± 0.03

<10e - 3

<0.5

943

serine/threonine kinase

11

0.11

0.07

1.57 ± 0.02

<10e - 5

<0.5

1138

cytochrome P450 like

26

0.23

0.22

1.06 ± 0.01

<10e - 4

<0.5

1833

pollen coat Protein

6

0.28

0.18

1.52 ± 0.06

<10e - 4

<0.1

0.32

0.20

1.63 ± 0.05

<10e - 4

<0.1

2453

mannose binding lectin

2

0.58

0.10

5.93 ± 0.28

<10e - 4

<0.5

2461

lectin/alpha -amylase inhibitor

98

-

-

12 values

-

-

2625

putative lipid transfer protein

24

0.26

0.21

1.26 ± 0.03

<10e - 4

<0.5

2687

R- protein

11

0.08

0.05

1.60 ± 0.04

<10e - 4

<0.5

3078

Ferredoxin

2

0.60

0.08

7.21 ± 0.47

<10e - 4

<0.5

3182

AsThi5

13

0.12

0.10

1.21 ± 0.02

<10e - 4

<0.5

0.24

0.18

1.30 ± 0.03

<10e - 4

<0.5

3384

lipid transfer protein

96

0.09

0.08

1.04 ± 0.02

<10e - 4

<1.0

0.16

0.09

1.43 ± 0.03

<10e - 4

<0.5

3677

Dof zinc finger transcription factor

2

0.17

0.15

1.14 ± 0.06

<10e - 5

<0.5

4479

S- locus Protein

16

-

-

11 values

-

-

5925

CCD1

2

0.35

0.33

1.08 ± 0.08

<10e - 4

<1.0

6716

beta- type phaseolin

13

0.07

0.06

1.21 ± 0.01

<10e - 5

<0.5

7274

Cystatin proteinase inhibitor

20

0.10

0.10

1.05 ± 0.02

<10e - 4

<1.0

7671

Beta expansins

31

0.18

0.15

1.21 ± 0.01

<10e - 5

<0.5

8102

Cathepsin D inhibitor

3

0.11

0.11

1.03 ± 0.01

<10e - 4

<0.5

8641

self incompatibility ribonuclease

139

-

-

25 values

-

-

9033

S- locus F- box protein

6

0.07

0.05

1.32 ± 0.01

<10e - 5

<0.5

9104

trypsin inhibitor

7

0.09

0.05

1.76 ± 0.02

<10e - 5

<0.5

0.13

0.12

1.05 ± 0.01

<10e - 4

<0.5

9154

LEA3

8

0.18

0.16

1.12 ± 0.02

<10e - 4

<0.5

16358

TIM23

2

0.34

0.30

1.12 ± 0.07

<10e - 4

<0.5

19762

seed maturation protein PM29

2

0.38

0.20

1.91 ± 0.09

<10e - 4

<0.1

34672

BudCAR6

2

0.29

0.25

1.15 ± 0.06

<10e - 4

<0.5

41180

serine/threonine kinase

28

0.09

0.09

1.10 ± 0.01

<10e - 5

<0.5

42513

LEA, cold response

2

0.44

0.25

1.78 ± 0.07

<10e - 4

<0.5

55717

putative transport protein SEC61

2

0.18

0.16

1.09 ± 0.07

<10e - 3

<1