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Pairwise Minkowski distances (a generalization of the Euclidian distance metric) between samples were computed on M′, and an unrooted neighbor-joining tree was constructed from the resulting n × n distance matrix, using the R package ape (http://ape-package.ird.fr/).fr/

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The significant difference between samples was computed using the Student's t test and correlation between variables using the Pearson correlation coefficient.

Geographic distances between all samples were computed with Geographic Distance Matrix Generator version 1.2.3 [ 126].

Pearson correlation coefficients and tests for correlation between paired samples were computed using the statistical software R. P-values were corrected for multiple testing using the Bonferroni method where appropriate.

Differences in nucleotide diversity between T1/T2 and T0 samples were computed to analyze the change in diversity during treatment (Figure 1).

The distance between two samples is computed using the Pearson Correlation based distance (5).

The relative difference in the level of H3K9Ac between the samples was computed as the change in the C1 relative to the D1 sample as log2 (C1/D1).

Values of environmental variables were first standardized and the Euclidean distance between the samples was computed using SPSS.

Spearman correlation between all samples was computed in order to examine the variance and the relationship of global gene expression across the samples, using genes with raw counts larger than zero.

We compare MCAP results with those offered by the classical AP approach (Frey and Dueck, 2007), where the similarities (negative distances) between the samples are computed as negative squared error distances (Frey and Dueck, 2007).

First of all the degree of concordance between FFPE and Fresh samples was computed considering all the variants called, including common polymorphism and novel variants mapping on the 37 Mb Exome target region.

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