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Figure 3 | BMC Evolutionary Biology

Figure 3

From: Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses

Figure 3

Test of hypotheses about the variation of ω along the phylogeny of DEF -like genes from the Orchidaceae. The table summarizes the hypotheses tested and their maximum likelihood estimates of ω, which depending on the hypothesis, are free to vary in specific clades (indicated on the phylogeny), while being uniform in the rest of the phylogeny. Column "L" indicates the likelihood value that corresponds to each hypothesis, and P the probability of each model rejecting its corresponding null hypothesis in the series of LRTs indicated at the bottom of the table. The phylogeny employed in these tests is based on the alignment of the complete coding sequences of DEF-like genes. However, to facilitate the inference of the parameters for each model, the outgroup and sequences from clades not directly relevant to the analyses were removed from the alignment and the phylogeny was re-estimated with an ad hoc model as described in Methods. The branches labeled with italics were tested for positive selection with branch-site models A1 and A.

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