For both datasets, the AU test revealed that the maximum likelihood phylogenies placing Isodiametra pulchra as most ancestral taxon, sister group to all remaining bilaterians (Fig. 1, Fig S1), was significantly better based on the available data (p>0.01) compared to trees in which the monophyly of the Platyhelminthes was enforced (Table S4).
Although Method 4 performed very well, Methods 2 and 3 should not be neglected because for a considerable number of datasets the maximum objective function values were obtained by these methods.
For yeast datasets the maximum intron size was set to 5,000.
In this transformed dataset, the maximum winds move from the coastal areas of Biscayne Bay through the Everglades northwesterly.
To check the frequency at which the true topology was reconstructed, we compared, for each dataset, the maximum a posteriori (MAP) topology of each segment against their respective true trees (i.e., the trees initially used to simulate the datasets).
To identify the outbreak threshold in the WS dataset, the maximum observed disease abundance was selected for each year and the overall mean and standard deviation of these maxima calculated.
For each dataset, the maximum clade credibility tree, which is the tree with the largest product of posterior clade probabilities, was selected from the posterior tree distribution after 10% burn in using the program TreeAnnotator version 1.4.8.
Each time (4095 repetitions corresponding to all 212 possible subject combinations, except for the actual dataset), the maximum number of consecutive significant latencies in the surrogate data was compared to the observed cluster size of 5 consecutive significant latencies.
Since the true value of δ is 0.2 in this dataset, the maximum normalised weight corresponds to the dataset no.
