By name: community-ecology-ordination description: "Performs multivariate community ecology analyses including ordination, diversity metrics, and assemblage comparisons. Use this skill when the user mentions species composition, NMDS, PCA ordination, PERMANOVA, beta diversity, alpha diversity, species richness, Bray-Curtis dissimilarity, indicator species analysis, cluster analysis, species-by-site matrices, diversity indices, or assemblage structure comparisons." skill_version: 1.0.0
Skill: community-ecology-ordination
Domain: NMDS · PCA · PCoA · Diversity · Clustering · Composition
Phase: 3 — Specialist
Used by: analyze-community-structure
Purpose
Guides the agent through multivariate analysis of ecological communities: ordination of species assemblages, diversity metric computation, beta diversity partitioning, cluster analysis, and hypothesis testing on community composition.
When to Invoke
- Analysing species composition across multiple sites
- Comparing community structure between treatments, habitats, or time periods
- Computing alpha and beta diversity metrics
- Identifying species groups or site clusters
Inputs
| Input | Format | Required |
|---|---|---|
| Species × site abundance or presence matrix | CSV | Yes |
| Environmental metadata per site | CSV | Recommended |
| Treatment or grouping variable | Factor column | Recommended |
Outputs
| Output | Description |
|---|---|
ordination_plot.png |
NMDS/PCA biplot |
diversity_metrics.csv |
Alpha diversity per site |
beta_diversity_matrix.csv |
Pairwise dissimilarity matrix |
permanova_results.txt |
PERMANOVA output |
cluster_dendrogram.png |
Hierarchical clustering dendrogram |
community_report.md |
Full analysis narrative |
Steps
1. Data Preparation
- Check for sites with zero species (remove or flag)
- Check for species observed at only one site (rare species handling: keep or remove)
- Standardise if needed (Hellinger, Wisconsin, presence/absence)
- Choose dissimilarity metric: Bray-Curtis (abundance), Jaccard (presence/absence), UniFrac (phylogenetic)
2. Alpha Diversity
- Species richness (S)
- Shannon index (H')
- Simpson index (1−D)
- Rarefaction curves to assess sampling adequacy
- Report metric ± SE per group
3. Ordination
NMDS:
- Run with k=2 (default) and k=3; choose lowest stress with acceptable fit
- Stress < 0.1 = excellent, < 0.2 = acceptable, > 0.2 = poor
- Run with ≥ 20 random starts; confirm convergence
PCA (for environmental gradients or species scores):
- Use Hellinger-transformed data or correlation matrix
- Report eigenvalues and % variance per axis
PCoA / MDS:
- For non-Euclidean dissimilarity matrices
4. Beta Diversity Partitioning
- Partition total beta diversity into nestedness and turnover components (betapart)
- Report contribution of each component per group comparison
5. Hypothesis Testing
- PERMANOVA (
adonis2): test if group centroids differ - PERMDISP: test if group dispersions (variances) differ (required before interpreting PERMANOVA)
- ANOSIM: alternative non-parametric test
- Report F/R statistic, R², p-value (permutation-based)
6. Species Contributions
- SIMPER: identify species driving dissimilarity between groups
- IndVal: identify indicator species per group
- Report top N contributing species per axis or group
7. Cluster Analysis
- Hierarchical clustering: Ward.D2 linkage preferred
- Cophenetic correlation to assess cluster quality
- k-means as alternative for large datasets
- Determine optimal k using silhouette or elbow method
Decision Points
| Condition | Diagnosis | Recommended Action |
|---|---|---|
| n_sites < 5 per group | Insufficient replication for PERMANOVA | Report descriptive statistics only; do not run hypothesis tests |
| NMDS stress > 0.2 | Ordination distorting community distances | Increase NMDS dimensions to 3; or reduce species set by removing very rare species |
| NMDS stress > 0.3 | Ordination is unreliable | Do not use NMDS; switch to PCoA or PCA on transformed data |
| Species occurring in < 5% of sites | Rare species inflating beta diversity | Apply rarity filter or downweight with Hellinger/Wisconsin transformation |
| PERMANOVA significant but PERMDISP also significant | Group dispersion differs (not only composition) | Report both results; interpret composition difference cautiously |
Key Decisions to Document
- Dissimilarity metric and rationale
- Rare species handling
- Data transformation applied
- Number of NMDS dimensions
- Permutation count for PERMANOVA
Tools and Libraries
R: vegan, betapart, indicspecies, ape, dendextend, ggplot2
Python: skbio, scipy.cluster, sklearn.manifold
Resources
resources/dissimilarity-metric-guide.md— which metric for which data typeresources/nmds-interpretation-guide.md— how to read and report NMDS plotsexamples/— worked NMDS and PERMANOVA example
Notes
- Always run PERMDISP before interpreting PERMANOVA; significant dispersion differences can inflate PERMANOVA results
- Stress value must be reported alongside all NMDS plots
- Rarefaction is mandatory when sites have very different sampling intensities