Instead, the number of clocks was in a first approach selected using an idea based on the gap statistic [26]: if there were actually k* clocks on the tree, then for kgroups of branches, and the algorithm would not assign branches as it "should".
For the taxon-rich exon 8 alignment, ω was also estimated for individual branches and groups of branches [ 38].
Most importantly, in hypothesis H4 where ω is estimated for each group of branches, these values converge and indicate that although all clades tested are under strong purifying selection, the group of branches in orchid clade C2 has an ω value of 0.1978, which is more than twice those estimated for other groups of branches.
Therefore, patterns of substitutions are significantly more different between the two groups of paralogous genes than between two random groups of branches.
Stages I, II, and III (shown in blue, pink and green, respectively) represent groups of branches from the alveolate ancestor to apicomplexan lineage ancestors.
We also apply the clade model (Bielawski and Yang 2003), which allows different groups of branches (clades) to have different ω's.
To compare patterns of substitution across the mitochondrial genome for select branches or groups of branches, we first divided substitution estimates for each window by the median substitution rate across all windows.
Briefly, we tested the null model assuming equal ω across branches and several nested models allowing for different ω ratios for particular groups of branches and compared the log likelihoods under these models with a likelihood ratio test [LRT, [ 19]].
Three models were examined; one with all branches evolving at the same rate (μ1 = μ2 = μ3), one with just the Bc group evolving at a separate rate (μ1, μ2 = μ3) and one with each of the three groups of branches evolving at separate rates (μ1, μ2, μ3).
