Fig 1.
Epoch model fit to binary trait data.
The epoch model describes the transition rates between traits (red and black) where a single shift at a point in time on the phylogeny results in a change in the overall transition rates. In this case, we observe higher transition rates prior to the dashed black line–followed by relative stasis.
Fig 2.
Tree constructed using MrBayes; all branches were supported with 100% posterior probability. Clades are labeled as follows: SynPro (Synechococcus + Prochlorococcus + Cyanobium), LPP-B (“LPP group B”; Leptolyngbya + Nodosilinea + Synechococcus), AcTh (Acaryochloris + Thermosynechococcus), Osc (Oscillatoriales sensu stricto), SPM (Synechocystis + Pleurocapsa + Microcystis), NX (Nostocales sensu lato + others).
Fig 3.
Composite Tree Showing Branching Location of Rogue Taxa.
This consensus tree summarizes the results of the rogue taxa addition and subtraction experiments. Lineages in bold indicate clades found in the core tree. The * indicates the clade of taxa that contain an intron in the tRNA-Leu gene and an intein in the DnaE protein. Distinct clades of rogue taxa are indicated with colored boxes: red shows the Octopus Spring clade, blue the Synechococcus elongatus clade, and green the Pseudanabaena clade.
Table 1.
Ranges of estimated node ages† for major cyanobacterial clades.
Table 2.
Epoch model fits and phylogenetic signal.
Fig 4.
Location of Support for a Shift for Each of 25 Phenotypic Traits.
The width and color intensity of each violin plot is proportional to the increase in support (likelihood units) for the epoch-model over the constant rate model (taken as the median for each time point over 2 sets of 10 trees taken from the posterior distribution of two different taxa sets). Points indicate the location of the maximum likelihood estimate for the location of the time-shift. Gray bars indicate the location of the Great and Neoproterozoic Oxidation Events. On the far right, the cumulative likelihood support is depicted (with all values <6 likelihood units less than the maximum set to 0). Two sets of major peaks can be found at 1.7 Ga and 0.6 Ga.
Table 3.
Inferred node ages and associated morphological and ecological traits† .
Fig 5.
Ancestral State Reconstruction of Morphology and Freshwater Habitat Salinity.
Reconstruction of binary traits for morphology (a) and freshwater habitat salinity (b), where the node color indicates the probability of the inferred character state. Branch lengths in the trees are proportional to time and the geologic age scale is shown at the bottom (with ages in Ma).