Within each run, task blocks (three per run; 135 seconds each) alternated with short fixation blocks (four per run; 30 seconds each).
The iTRAQ method was used with LC-MS/MS to allow multiplexing of samples (up to eight per run), which not only saves time but also reduces technical variability.
Samples were multiplexed to combine either eight or ten samples per run.
Analyses with MrBayes were performed over two runs, including four chains and three million generations per run.
We estimated gene trees using MrBayes 3.1.2 [ 58], with two runs and four chains (one cold, three heated) per run.
We partitioned the data by codon position and performed two independent runs with five chains per run, sampling trees every 100 generations for 2 million generations.
For the sequencing we performed 13 Genome Sequencer FLX runs, which produced over 558 million bases and 1.43 million reads per run.
The analysis was run twice, with 20 million generations per run (total 40 million generations).
Each session consisted of two runs per concentration and two passes per run.
The Riverside panel included eight 10-day runs with four subjects per run.
