Figure 1.
Phylogenetic relationships within the long branch clade in Annonaceae.
a) Phylogram of the majority rule consensus tree of the last 30,000 trees sampled after five million generations of the MCMCMC run indicating the branch lengths as well as the two major groups recognized within the Annonaceae: long branch and short branch clade. b) Majority rule consensus tree of the last 30,000 trees sampled after five million generations of the MCMCMC run. Posterior probabilities under 0.95 are displayed at nodes. Thick branches indicate support >0.95 PP. The distribution of species with compound pollen (1, black squares) and syncarpy (2, black squares) are represented along the tips of the phylogeny. Missing squares indicate absent observations; the species was scored as uncertain for that character.
Table 1.
Average number of transformations estimated for each combination of the mean rate value (E(T)) and the level of confidence (SD(T)) estimated after 1000 simulations on the 201 last trees sample from the MCMC run.
Figure 2.
Posterior probability density distributions of the transformation rate θ for the pollen unit character.
Posterior probability density distributions of each rate category given each combination of E(T) and SD(T) for the pollen unit character. The bars of the histogram represent the posterior distribution densities given the prior and the data for each rate category. The continuous gamma distribution was made discrete by breaking it into 60 equally probable rate categories [33]. Each category is represented by the mean of the portion of the gamma distribution included in the rate category. The total area of the histogram as well as the prior distribution equal one. The posterior density histograms are overlaid with the corresponding prior gamma density distribution (dashed) as well as a fitted curve (black). x-axis: rate of transformation. y-axis: density scale.
Figure 3.
Posterior probability density distributions of the transformation rate θ for the carpel fusion character.
Posterior probability density distributions of each rate category given each combination of E(T) and SD(T) for the carpel fusion character. The bars of the histogram represent the posterior distribution densities given the prior and the data for each rate category. The continuous gamma distribution was made discrete by breaking it into 60 equal probable rate categories [33]. Each category is represented by the mean of the portion of the gamma distribution included in the rate category. The total area of the histogram as well as the prior distribution equal one. The posterior density histograms are overlaid with the corresponding prior gamma density distribution (dashed) as well as a fitted curve (black). x-axis: rate of transformation. y-axis: density scale.
Figure 4.
Posterior probabilities for both pollen unit and carpel fusion characters.
Posterior probabilities for each rate prior E(T) given a standard deviation S(T) for both pollen unit and carpel fusion characters. x-axis: rate of transformation. y-axis: sampling frequency ( = posterior probability) of each discrete rate category.
Figure 5.
Posterior probabilities for all inferred character histories for the pollen character.
Negative logarithm (base 10) of the posterior probabilities for all character histories that have occurred during the simulation for the pollen character and the combinations E(T) = 1, 5 and 10 and SD(T) = 1 and 5. The x-axis represents the total number of transformations from 1 to 0 (i.e. number of gains) and the y-axis from 0 to 1 (i.e. number of losses). It is important to note that as we used the negative logarithm thus the lowest values (dark red) represent the highest PPcs. The colours for the PPc are not the same across the graphs, as they represent the values for each independent analysis.
Figure 6.
Posterior probabilities for all inferred character histories for the carpel fusion character.
Negative logarithm (base 10) of the posterior probabilities for all character histories that have occurred during the simulation for the carpel fusion character and the combinations E(T) = 1, 5 and 10 and SD(T) = 1 and 5. The x-axis represents the total number of transformations from 1 to 0 (i.e. number of gains) and the y-axis from 0 to 1 (i.e. number of losses). It is important to note that as we used the negative logarithm thus the lowest values (dark red) represent the highest PPcs. The colours for the PPc are not the same across the graphs, as they represent the values for each independent analysis.
Table 2.
The first six character histories with the highest posterior probability (PPc) for each combination of E(T) = 1 and 5 and their respective SD(T).
Table 3.
The first six character histories with the highest posterior probability (PPc) for each combination of E(T) = 10 and 15 and their respective SD(T).