Tree specific log linear model with branch diameter and branch length as covariates was used to obtain individual branch biomass.
We employed a relaxed molecular clock model with branch rates drawn independently from a lognormal distribution [62], ten time constraints (Table S5), and the reconstructed birth-death process [63] as a tree prior (see Fig. S4 for substitution rates).
Five hundred base pairs per locus were generated under the Jukes-Cantor (JC69) model with branch lengths scaled by 0.005 to convert coalescent units to mutation units.
Mr Bayes was run using a GTR plus gamma model, with branch length unconstrained, branch length priors set to an exponential distribution with a parameter of 10, and shape parameter priors set to an exponential distribution with a parameter of 10.
Purifying selection, selective removal of (deleterious) variations, is likely the main force acting on this clade, as suggested by low dN/dS values (one-rate model for whole groups: bCRK-I 0.184, bCRK-II 0.192, PDLPs 0.267, sdCRRSPs 0,162, CRCK 0.134; more flexible model with branch-specific dN/dS within each group yielded similar results).
The CC is defined as the computational time needed to generate the output of the GPH model with branches, normalized by the computational time needed to generate the output of a GPH model for (linear system case).
The evolution of floral size (PC1) was best described by the multi-rates BM model with branch-specific rates (Table 1).
For DF2, models with equal branch lengths provided a better fit to the data than any other model, but it was not possible to distinguish between nonphylogenetic and punctuated models (AIC differences <2; Table 3).
While the under-determined nature of the two-branch model is unlikely to repeat in more complex models with more branches, the optimization procedure applied to this two-branch model is equally applicable to over-determined systems.
Some modelers use single compartment models, others use models with simplified branching structure that may require from 2 to a dozen or so compartments, and others focus on detailed morphologies that require hundreds or thousands of compartments, depending on the cell type.
