with a standard curve prepared from a purchased sequencing library (Illumina). Samples were multiplexed so that each behavioral group was represented in each flow cell of the sequencer. 10nM of each library was pooled together in four multiplex libraries and sequenced on an IlluminaHiSeq 2000 instrument during a single-end 50 cycles sequencing run by the Genomics High-Throughput Facility (GHTF) at the University of California, Irvine. The resulting sequencing data for each library were post-processed to produce FastQ files, then demultiplexed and filtered using both Illumina software CASAVA 1.8.2 and in-house software. Control reads successfully aligned to the PhiX control genome or poor quality reads failing Illumina's standard quality tests were removed from the following analyses. The quality of the remaining sequences was further assessed using the PHRED quality scores produced in real-time during the base-calling step of the sequencing run (Supplemental FigS6A).
