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Table 1 Quantitative group comparisons using ANOSIM and PCoA to analyze large effect sizes (between environments) of simulated and unsimulated human saliva and public restroom floor samples

From: ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

 

Test statistic (R)

p value

% explained

Unsimulated (real) data community analysis

   

   Jaccard (Fig. 2a)

0.865

0.001

31.24

   Bray-Curtis (Fig. 2b)

0.849

0.001

47.17

   Unweighted UniFrac with FastTree (Fig. 2c)

0.734

0.001

43.56

   Weighted UniFrac with FastTree (Fig. 2d)

0.263

0.001

63.52

   Unweighted UniFrac with ghost-tree (Fig. 2e; Additional file 1: Figure S1A)

0.753

0.001

50.79

   Weighted UniFrac with ghost-tree (Fig. 2f; Additional file 1: Figure S1B)

0.463

0.001

76.21

   Unweighted UniFrac with ghost-tree 0 branch foundation (Additional file 1: Figure S1C)

0.730

0.001

50.61

   Weighted UniFrac with ghost-tree 0 branch foundation (Additional file 1: Figure S1D)

0.458

0.001

76.91

   Unweighted UniFrac with ghost-tree 0 branch extensions (Additional file 1: Figure S1E)

0.700

0.001

66.11

   Weighted UniFrac with ghost-tree 0 branch extensions (Additional file 1: Figure S1F)

0.453

0.001

67.97

Simulated data community analysis

   

   Jaccard to analyze FTSCs (Fig. 3a)

0.191

0.001

3.05

   Bray-Curtis to analyze FTSCs (Fig. 3b)

0.191

0.001

2.71

   Jaccard to analyze GTSCs (Fig. 3c)

0.036

0.001

1.63

   Bray-Curtis to analyze GTSCs (Fig. 3d)

0.036

0.001

2.43

   Unweighted UniFrac with FastTree to analyze FTSCs (Fig. 3e)

0.675

0.001

22.10

   Weighted UniFrac with FastTree to analyze FTSCs (Fig. 3f)

0.255

0.001

43.69

   Unweighted UniFrac with FastTree to analyze GTSCs (Fig. 3g)

0.298

0.001

68.87

   Weighted UniFrac with FastTree to analyze GTSCs (Fig. 3h)

0.150

0.001

54.08

   Unweighted UniFrac with ghost-tree to analyze FTSCs (Fig. 3i)

0.302

0.001

27.72

   Weighted UniFrac with ghost-tree to analyze FTSCs (Fig. 3j)

0.117

0.001

35.55

   Unweighted UniFrac with ghost-tree to analyze GTSCs (Fig. 3k)

0.580

0.001

20.40

   Weighted UniFrac with ghost-tree to analyze GTSCs (Fig. 3l)

0.307

0.001

44.98

  1. Note: For unsimulated samples, sample size is 36, and two groups were analyzed using 999 permutations. For simulated samples, sample size is 360, and two groups were analyzed using 999 permutations. The test statistic (R), p value, and percent variation explained in the first the PCoA axes are presented for each comparison