Table 2

Comparison of alternatively parameterized models of evolution indicates significant departure from neutrality at an early stage of duplicate gene evolution.

Comparison

# bp

-lnL Ho

-lnL Ha

P value

Fixed Ka/Ks ratio in early lineage in null model

Estimated Ka/Ks ratio in other lineages in null model

Estimated Ka/Ks ratio in early lineage in alternative model

Estimated Ka/Ks ratio in other lineages in alternative model


Fig. 1B

80856

-166032.2641

-165608.1273

0.0000

1

0.1322

0.158

0.1415

Fig. 1C

9717

-15716.3195

-15698.0601

0.0000

1

0.2261

0.1242

0.228

Fig. 1D

6966

-13235.97398

-13187.03582

0.0000

1

0.141

0.1052

0.1557

Fig. 1B (partitioned)

80856

-160755.0615

-160071.0687

0.0000

1

NL

NL

NL

Fig. 1C (partitioned)

9717

-15436.44329

-15413.5068

0.0000

1

NL

NL

NL

Fig. 1D (partitioned)

6966

-13077.6404

-13016.5679

0.0000

1

NL

NL

NL


Likelihoods of a null model with the Ka/Ks ratio fixed at one at an early stage of duplicate gene evolution and an alternative model with this ratio estimated are indicated. Species acronyms are the same as in Fig. 1 and abbreviations are the same as in Table 1.

Chain et al. BMC Evolutionary Biology 2008 8:43   doi:10.1186/1471-2148-8-43

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