Moving from the simple two population case, we modeled different extreme time sampling scenarios from individuals belonging to a single global population (Fig. 5): (i) contemporaneous samples (i.e., assuming no heterochrony), (ii) regular, (iii) uniform and (iv) exponential sampling across time.
The overnight cultures were diluted 1 20 and grown at 30°C for 4 hr, to OD600 of approximately 0.3, and used as the "exponential" samples.
The estimated conditional Type I error probabilities are summarized in Table 1 (right): For exponential samples, only a negligible tendency towards conservative decisions was observed, but samples from the uniform distribution, and, to a lesser extent, samples from the normal distribution proved problematic.
To front weight our calculation of support statistics, we used a base-two exponential sampling distribution: in addition to the initial state (1 partition), we sampled submatrices at 2, 4, 8, 16, 32, 64, and 128 partitions for our LS calculations.
Ribosome profiling yielded 3.75 and 2.55 million sequencing reads aligning to annotated protein-coding sequences for the exponential phase sample and the biofilm entry sample, respectively.
Median ribosome density across all protein coding sequences was computed for the 60 nt region around each of six Shine-Dalgarno-like trinucleotide sequences (Li et al., 2012 ) for the exponential phase sample (left-hand panel) and the biofilm entry sample (right-hand panel).
Therefore, we calculated the median ribosome density at each of the 61 sense codons across the 1556 protein-coding sequences in the exponential phase sample and the 1148 sequences in the biofilm entry sample that had an average coverage greater than one sequencing read per codon.
One 2D LC/MS/MS run (20 x 1 h runs) (Dwivedi et al., [2008]) was conducted on an exponential phase sample from cells grown in low glycerol (170 mM) (see Additional file 1), primarily to survey the microorganism's proteome for future cross-organism and RNAseq studies.
For SDS-PAGE, equivalent volumes of cell extract (5.6 µL of protein from exponential phase samples and 1.6 µL of protein from stationary phase samples) or culture supernatant (54 µL of 2X sample) were resolved by 12% or 10 20% SDS-PAGE (Protean II gel, Bio-Rad).
If the covariance function is squared exponential, then sampled functions smoothly fluctuate.
