Growth rates of grass species with contrasting photosynthetic pathways and life histories

A phylogeny for the species involved in the growth analysis was reconstructed using a set of sequences from four regions of the chloroplast genome that have been widely used in grass phylogenetics: trnKmatK, rbcL, ndhF and trnLtrnF. These markers were retrieved from NCBI databases when available for the species used here, and were amplified and Sanger sequenced using published protocols for species that had never been analysed. Each marker was then aligned using MUSCLE v.3.8.31, and the alignment was manually verified. The four markers were then concatenated, and a time-calibrated phylogenetic tree was inferred using Beast v1.8.4. The GTR+G+I substitution model was used, and the speciation prior was set to a Yule process. A relaxed molecular clock with a log-normal distribution was used. The monophyly of each of the BOP and PACMAD clades was enforced to root the tree, and the split of the two clades was constrained by a normal distribution with a mean of 51.2 and a standard deviation of 0.0001. Two analyses were run for 10,000,000 generations, with sampling frequency of 1,000 generations. Convergence of the runs and effective sampling sizes were monitored with Tracer v1.6, and the burn-in period was set to 5,000,000. Posterior trees from the two analyses were combined, and median ages were mapped on the highest credibility tree, which was used for comparative analyses.