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We tested the partitioning of genetic variation across three different sampling groupings according to: (1) the four phylogenetic clades, as outlined above; (2) four geographic regions: the Andean foothills, western Amazonia, south Amazonia and north Amazonia, which largely mirror the geographic distribution of haplotypes within clades; and, (3) ecoregions.
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Equation (2) is empirically estimated using several sample groupings.
The reconstructed NMR spectra elucidate the reasons for the sample groupings.
To test for differential representation of microbial taxa in different samples and sample groupings the Deseq2 package (Love et al. 2014) was used in conjunction with Phyloseq (McMurdie and Holmes 2013).
Since the first and second components combined usually describe > 50% of the variance within the dataset, meaningful conclusions regarding sample groupings can often be obtained from this plot, prior to quantitative analysis by LC.
To examine the robustness of the sample groupings, we used Significance of Clustering (SigClust) [51].
Calculations were performed separately for each of the three sample groupings.
This can be observed for random sample groupings irrespective of microwave treatment.
Although the most variance is accounted for by PC1 (29.83%), the segregation of the sample groupings is observed along PC2.
Data quality, batch effect, and sample groupings were assessed by Principle Component Analysis (PCA) with correlation dispersion matrices.
This produces a two-level hierarchy of sample groupings containing the facets and sub-facets (Additional file 2: Table S2).
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