Grazing exclosures were paired with sites grazed both the first and second growing seasons following the fire and replicated across loamy and sandy ecological sites.
Thus, we generated four datasets named HD_Mix_45 (five replicates following the mixture data model with heritability 0.45), HD_Mix_10 (five replicates following the mixture data model with heritability 0.10), HD_One_45 (five replicates following the one normal data distribution with heritability 0.45) and HD_One_10 (five replicates following the one normal distribution with heritability 0.10).
This was performed by first deriving a dispersion model describing variances of fragment counts across replicates, which was then used to calculate the variances on a gene's relative expression across replicates following the method described in [ 70] (Additional file 3: Figure S2, Additional file 4: Figure S3 and Additional file 5: Figure S4).
We generated 100 bootstrap replicates and inferred event rates for each replicate, following the full four-stage estimation procedure described above.
The relative quantification method (2-ΔΔ C T) was used to evaluate quantitative variation between the 3 replicates, following the method of Livak and Schmittgen [ 38].
For each value of K, which is the number of genetically distinct populations, the Markov chain Monte Carlo scheme was run with a burn-in period of 10 000 steps and a chain length of 100 000 replicates following the non-admixture model.
Acetyl bromide lignin was determined in triplicate for all of the miscanthus samples (25 lines × 3 time points × 2 tissues × 3 plant replicates) following the general procedures described by Foster et al. (2010) and Fukushima and Hatfield (2004), with some modifications, described as follows.
Satire always ends up following the news agenda and replicating its institutional biases - for example, the habit of ignoring issues to talk about power-play, intrigues and the whole wretched soap opera of Westminster gossip.
Two replicate RNA extractions per line were conducted on random subsamples of thirty 3-day-old males per replicate, following the same protocol as in the MA lines.
Messenger RNA, cRNA synthesis and labelling reactions were performed independently for each replicate following the recommendations of the Gene Chip® Expression Analysis technical manual (Affymetrix, Santa Clara, CA).
The AFLP analysis was performed in replicate following the ligation of the DNA for each individual using a modified version of Vos et al. [ 62] to generate approximately 300 loci.
