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Table 1 Comparison of alternatively parameterized models of evolution in Fig. 1 indicates no significant difference in the Ka/Ks ratio at an early and a later stage of duplicate gene evolution.

From: Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

Comparison # base pairs -lnL Ho -lnL Ha P value Ka/Ks combined early and late Ka/Ks ratio early Ka/Ks ratio late Ka/Ks diploid
Fig. 1B 80856 -165602.720 -165602.386 0.414 0.164 0.158 0.169 0.126
Fig. 1C 9717 -15699.366 -15697.250 1.000 0.208 0.124 0.346 0.198
Fig. 1D 6966 -13187.865 -13186.872 0.160 0.126 0.187 0.105 NA
Fig. 1B (partitioned) 80856 -160085.863 -159889.926 1.000 NL Af2 Af2 NL
Fig. 1C (partitioned) 9717 -15400.349 -15393.089 0.888 NL Af2 Af2 NL
Fig. 1D (partitioned) 6966 -12983.343 -12978.034 0.807 NL Af2 Af2 NA
  1. Indicated for comparisons depicted in Fig. 1B, C and D are likelihoods of the null model (early and later Ka/Ks are the same) and the alternative model (early and later Ka/Ks are not the same), the one-sided probability of the Ka/Ks ratio being higher in the early stage, and the Ka/Ks ratios estimated from each of these models. For the first two tests, the Ka/Ks ratio of the diploid lineage was estimated using a different model where a unique Ka/Ks ratio was estimated for each branch (a free ratio model). Also listed are the joint likelihoods of these models from an analysis partitioned by gene fragment. For the partitioned analyses, Ka/Ks ratios for each fragment are either listed in Additional file 2 (Af2), not listed (NL), or not applicable (NA).