Spine length is depicted as squares over branches in the phylogeny, and the associated parasite prevalence is depicted in circles.
Using the estimated ages of fossils of 17 flowering plants, including the few known orchid specimens, they were able to date the main branches in the phylogeny and calculate the rate at which new species appeared.
The most important advantage of parametric methods is their ability to integrate into the biogeographic inference estimates of the evolutionary divergence between lineages or the time since cladogenesis, which are represented by the length of branches in the phylogeny (Fig. 4b).
The 'one-ratio' model assumes the same ratio for all branches in the phylogeny.
We treated branch B as the foreground branch and all other branches in the phylogeny as background branches (Figure 2A).
The simplest model, referred to as null hypothesis H0, assumes the same ω ratio for all branches in the phylogeny.
Branch models [23] that allow ω to vary among branches in the phylogeny were applied to determine ω ratios on particular lineages.
The likelihood ratio test failed to reject the null hypothesis that the mutation rate is homogeneous among all branches in the phylogeny (LR = 4.14 and p = 0.902).
Although almost 2000bp of sequence data were analyzed for the taxa included here, phylogenetic relationships at deeper branches in the phylogeny remain only poorly resolved.
The data support 14 discrete evolutionary events (gains or losses) distributed among 24 branches in the phylogeny, with 0, 1, or 2 events per branch (Figure 10).
To calculate the dN/dS ratio at lineages (defined as all branches in the phylogeny, both terminal species nodes and internodes), sequences associated with species-specific premature stop codons were removed.
