Fig. 4: Predictive ability of ESL-PSC genetic models of C4/C3 photosynthesis.

Sequence (trait) prediction scores (SPS, see Methods) from model ensembles are shown for known C4 (blue) and C3 (red) species in kernel density estimation plots. Negative SPS indicates a prediction of the C3 (trait-negative), and positive SPS indicates a prediction of the C4. Predictions shown are for: a all species, b species in clades independent of the clades contributing species for model building, c response-flipped null ESL-PSC models of C4/C3 photosynthesis. Null models were constructed by flipping the trait response values of 3 out of 6 of the input contrast pairs. This was done for all 10 distinct combinations of 3 out of 6 contrast pairs, and all model predictions were aggregated. d Pair-randomized null ESL-PSC models of C4/C3 photosynthesis. Null models were constructed by randomly flipping or not flipping the residues between each species contrast pair at every variable residue in the MSA. For each of the 25 alternative PSC input species combinations, randomized pair-flipped alignments were generated, and model ensembles were produced for each. Aggregated predictions are shown.