PERMANOVA genus beta diversity by study group

Bray–Curtis dissimilarity on genus relative abundance; study-group effect tested with permutational MANOVA.

1 Research question

Does study group explain differences in genus-level community composition?

Null: Multivariate centroids do not differ among study groups (PERMANOVA on Bray–Curtis distances).

2 Data

• Response: Genus relative abundance (g__* columns after wide reshape).
• Predictor: Study_group_new.
• Input: data/processed/genus.csv (long format from make save; pivoted in this post).

3 Methods

Item	Choice
Test	PERMANOVA (vegan::adonis2)
Distance	Bray–Curtis
Formula	dist ~ Study_group_new
Permutations	999
Visualization	PCoA (cmdscale, k = 2), 95% ellipses

4 Results

Term	Df	Sum of squares	R²	F	Pr(>F)
Model	2	0.1846	0.1083	0.7896	0.852
Residual	13	1.5195	0.8917	NA	NA
Total	15	1.7041	1.0000	NA	NA

Study group explained 10.8% of variance in Genus composition (R² = 0.108; pseudo-F = 0.79; p = 0.8520, 999 permutations).

5 Figure

plot_pcoa_study_group(
  fit$dist,
  fit$metadata,
  permanova_result,
  cfg$label
)

Figure 1: PCoA of genus Bray–Curtis dissimilarity by study group.

6 Reproducibility

• Helpers: stats/R/permanova_helpers.R
• Pipeline: make wrangle → make save