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.
Fam- Nr.
 Description
 Size
 Ka
 Ks
 Ka/Ks
 p- value
 Bon*
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

Roth and Liberles BMC Plant Biology 2006 6:12   doi:10.1186/1471-2229-6-12