Likelihood ratio tests showed that all but a few branch lengths were significantly greater than zero, and an additional likelihood ratio test rejected the molecular clock hypothesis.
In model 2 (M2), a continuous positive selection model with an additional (third) ratio of nonsynonymous to synonymous substitutions (ω2) estimated from the data, ω2 is 3.17, but represented only a small proportion (p2 = 0.08 out of 1.0) of codon sites.
We also identified differences in the gene expression pattern between samples stored at –80oC and in liquid nitrogen, with 2,193 differentially expressed genes (551 genes with an additional 0.5log2 ratio cut-off), but the FDR stayed relatively high (35%).
Model M1, a neutrality model that constrained ω to be either 0 or 1, was compared to both M2, a selection model that added an additional ω ratio class estimated from the data, and M3, a selection model that used an unconstrained discrete distribution to model classes of ω ratios.
The influence of the additional ratio of MSWI BA to MSW on the degradation of the landfilled refuse was also discussed.
Including 'block' and the 'strain-by-block' interaction (with 'block' nested within 'lab') in the GLM, allowed us to calculate an additional F-ratio by dividing the mean squares (MS) of the 'strain-by-lab' interaction by the MS of the 'strain-by-block' interaction (F = MS strain×lab)/MS strain×block(lab))).
The second alternative model (three ratios) assumed an additional, collective ω ratio for the branches leading to the three male-biased paralogs, and the third alternative model (five ratios) assumed a distinct ω for each branch leading to a male-biased paralog or clade.
Besides the earlier mentioned categorization in groups 0 2 an additional ERaD7 expression ratio was defined with two groups: ERaD7/ ERa standard mRNA ratio >0.5 and ERaD7/ ERa standard mRNA ratio ≤0.5.
