For many taxa the differences in abundance between burned and unburned sites were maintained even when controlling for litter availability and quality.
Finally, to provide functional insights over the orthologs that S. meliloti shares with proteobacterial and nonproteobacterial taxa, the differences between hits on nonproteobacterial and proteobacterial taxa were computed for each COG category.
In the consensus setting, i.e., where all data sets contain the same taxa, the differences between concatenated alignments and tree combination have been extensively discussed (e.g. [ 22- 27]).
To identify the taxa explaining the differences between the different stations, SIMPER analyses were carried out both on presence/absence and square-root transformed data using Bray-Curtis similarity with a 90% cut-off for low contributions.
Results showed that the trees based on the three independent codon positions and the entire codons were largely congruent with each other in most taxa; the major difference was observed in the positions of F. bidentis and F. angustifolia.
Although both observations suggest that the genome size is a poor predictor of the functional content of a genome, our finding highlights another aspect: the number of sites of crucial functional importance may be unexpectedly constant across taxa, despite the differences in the number of genes and the length of the coding regions (Alexander et al. 2010; Howe et al. 2013).
Looking at the weighted number of each PPIase family in these two taxa, this difference appears due to a reduced number of cyclophilins and FKBPs within the Pezizomycotina fungi.
For the coding of leucine, UUR-codons are more frequently used in all chelicerate taxa than CUN-codons, but the difference is by far higher in those taxa, which show the highest AT-contents (The acarid taxa Haemaphysalis flava, Amblyomma triguttatum, Varroa destructor, Rhipicephalus sanguineus, and the pycnogonid Nymphon gracile).
If α = 0.05 is used as the cutoff for statistical significance, and divided by ten to yield a Bonneferroni-corrected threshold of 0.005, then in only three out of ten classes (15 taxa / 2 edits, 20 taxa / 2 edits, and 30 taxa / 2 edits) is the difference between experimental and random trees statistically significant.
P. rus was found to be relatively abundant at Sites 1 and 2 (43% and 20%, respectively), and was shown to be among the most important taxa contributing to the differences among sites (Table 3).
