The amount of nitrogen used for photosynthesis governs molecular evolution in plants

Background: Genome and transcript sequences are composed of long strings of nucleotide monomers (A, C, G and T/U) that require different quantities of nitrogen atoms for biosynthesis. Results: Here it is shown that the strength of selection acting on transcript nitrogen content is determined by the amount of nitrogen plants require to conduct photosynthesis. Specifically, plants that require more nitrogen to conduct photosynthesis experience stronger selection on transcript sequences to use synonymous codons that cost less nitrogen to biosynthesise. It is further shown that the strength of selection acting on transcript nitrogen cost constrains molecular sequence evolution such that genes experiencing stronger selection evolve at a slower rate. Conclusions: Together these findings reveal that the plant molecular clock is set by photosynthetic efficiency, and provide a mechanistic explanation for changes in plant speciation rates that occur concomitant with improvements in photosynthetic efficiency and changes in the environment such as light, temperature, and atmospheric CO2 concentration.