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

Microbiome

Table 2 Quantitative group comparisons using ANOSIM to analyze small effect sizes (within environments) of simulated human saliva and public restroom floor samples

	Test statistic (R)	p value
Restroom samples
Non-phylogenetic methods
Jaccard to analyze FTSCs	0.225	0.001
Bray-Curtis to analyze FTSCs	0.239	0.001
Jaccard to analyze GTSCs	0.053	0.001
Bray-Curtis to analyze GTSCs	0.056	0.001
FastTree
Unweighted UniFrac with FastTree to analyze FTSCs	0.673	0.001
Weighted UniFrac with FastTree to analyze FTSCs	0.798	0.001
Unweighted UniFrac with FastTree to analyze GTSCs	0.038	0.057
Weighted UniFrac with FastTree to analyze GTSCs	-0.001	0.518
ghost-tree
Unweighted UniFrac with ghost-tree to analyze FTSCs	0.125	0.001
Weighted UniFrac with ghost-tree to analyze FTSCs	0.073	0.001
Unweighted UniFrac with ghost-tree to analyze GTSCs	0.619	0.001
Weighted UniFrac with ghost-tree to analyze GTSCs	0.655	0.001
Saliva samples
Non-phylogenetic methods
Jaccard to analyze FTSCs	0.250	0.001
Bray-Curtis to analyze FTSCs	0.253	0.001
Jaccard to analyze GTSCs	0.032	0.001
Bray-Curtis to analyze GTSCs	0.032	0.001
FastTree
Unweighted UniFrac with FastTree to analyze FTSCs	0.852	0.001
Weighted UniFrac with FastTree to analyze FTSCs	0.756	0.001
Unweighted UniFrac with FastTree to analyze GTSCs	0.031	0.001
Weighted UniFrac with FastTree to analyze GTSCs	0.023	0.001
ghost-tree
Unweighted UniFrac with ghost-tree to analyze FTSCs	0.125	0.001
Weighted UniFrac with ghost-tree to analyze FTSCs	0.068	0.001
Unweighted UniFrac with ghost-tree to analyze GTSCs	0.524	0.001
Weighted UniFrac with ghost-tree to analyze GTSCs	0.596	0.001

Note: For restroom sample diversity metrics, sample size is 160, and 16 groups were analyzed using 999 permutations. For saliva sample diversity metrics, sample size is 200, and 20 groups were analyzed using 999 permutations

ISSN: 2049-2618