Four main geographic groupings are observed in the phylogram.
Although the most variance is accounted for by PC1 (29.83%), the segregation of the sample groupings is observed along PC2.
Using the codon bias of ribosomal ORFs as a reference, a pattern similar to that of the highly expressed genes in the three different groupings was observed, but this tendency was clearly detected when the HV and AV grouping was compared.
Very similar groupings of genotypes were observed, e.g. the over-lapping genotypes in cluster 1 also group together in previous studies [ 17, 20], e.g. BTx3197 and BOK11 grouping tightly together in Menz et al. [ 17], in addition to RTx7000 and Btx3042.
Only minor differences in cluster groupings between analyses were observed where S. agnetis and S. hyicus formed a clade with S. chromogenes as the sister taxon in Additional file 7: Figure S5, while the alternate (non-clock BEST) analysis estimated S. agnetis and S. chromogenes to form a clade, sister to S. hyicus (data not shown).
Two distinct groupings of NNRTI drugs were observed based on the distribution of virtual phenotypes: etravirine (ETR), the newest member of this drug class, constituted one group, while all other NNRTIs (efavirenz [EFV], delavirdine [DLV] and nevirapine [NVP]) comprised the second.
Highly similar groupings of the isolates were observed when a dendrogram was built based on spoligotypes alone or on a combination of VNTR and spoligotypes, although the resolution was lower when spoligotyping was used alone (data not shown).
Where pedigree data was available, groupings associated with these pedigree relationships were observed.
Within the individual vertebrate clades, there was a clear separation of tetrapod and teleost genes, and only minor changes to the species tree were observed within these groupings (compare Figure 3 to Figure 1).
Thus, while trends were observed within certain clinicopathologic groupings, these trends did not consistently reach statistical significance in both the Pantomics TMA and the AMC sample sets.
