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Table 2 Unigenes under positive selection detected by the likelihood codon substitution models.

From: Sequence diversity in three tomato species: SNPs, markers, and molecular evolution

Analysis

Unigene

Annotation1

p-value2

Sites3

dn/ds4

dn/ds 15

dn/ds 26

lnL7

lnL28

LxH

SGN-U314303

Aldehyde dehygrogenase

0.00132

491

0.0665

0.0343

998.99

-3184.6

-3173.1

LxH

SGN-U317105

Unknown protein

0.00132

286

0.2677

0.0058

145.99

-1821.6

-1810.1

LxH

SGN-U315058

Tropinone reductase

0.00211

275

0.1361

0.0836

998.99

-1902.2

-1891.5

LxH

SGN-U315796

Alcohol dehydrogenase

0.00276

399

0.0924

0.0036

0.35

-2899.9

-2890.1

LxH

SGN-U317449

Fe(II)/ascorbate oxidase

0.00276

441

0.0569

0.0019

193.75

-2443.7

-2433.8

LxH

SGN-U317968

Hypothetical protein

0.00276

253

0.2771

0.0053

3.34

-1058.9

-1049.1

LxH

SGN-U319889

Putative kinesin light chain

0.00941

437

0.1566

0.0032

121.86

-1966.2

-1957.8

LxH

SGN-U314953

Unknown protein

0.01001

176

0.2633

0.0485

998.99

-1305.9

-1297.6

LxH

SGN-U318509

Hypothetical protein

0.03006

547

0.1026

0.0172

0.52

-2158.9

-2151.8

LxP

SGN-U314632

Ubiquitin extension protein 2/60S ribosomal protein L40

0.00099

155

0.0580

0.0017

998.99

-512.5

-500.2

  1. LxP – S. lycopersicum and S. pennellii analysis, LxH – S. lycopersicum and S. habrochaites analysis. 1Annotation – based on the annotation from the best BLAST hit in Arabidopsis thaliana. 2 p-value – Multiple testing corrected p-values for the differences in the maximum likelihood estimates of the two models fit. 3 Sites – number of codons analyzed, 4 dn/ds – dn/ds for the model where one dn/ds ratio is estimated for the entire evolutionary tree. 5 dn/ds 1 – dn/ds for the non S. lycopersicum lineages in the model where a different dn/ds ratio is estimated for the branch leading to S. lycopersicum. 6 dn/ds 2 – dn/ds for the S. lycopersicum lineage in the model with two dn/ds ratios. The very high dn/ds ratios observed for some genes are a consequence of relatively little diversity between wild and domesticated tomato and are likely to be an overestimate of the true rate. 7 lnL – likelihood estimate for the model with one dn/ds ratio. 8 lnL2 – likelihood estimate for the model with two dn/ds ratios.