Implement alpha and beta diversity analyses and statistical analysis of community composition

[jibarozzo]

Description:
Conduct comprehensive diversity analyses to understand community structure.

Tasks:
Alpha and Beta analyses

• Perform rarefaction curve analysis to assess sampling depth adequacy
• Calculate and visualize alpha diversity metrics (Shannon, Simpson, Observed ASVs)
• Calculate beta diversity distances (UniFrac, Bray-Curtis, Jaccard)
• Create ordination plots (PCoA, NMDS) to visualize community differences
• Test for significant groupings by environmental factors

Statistical analyses

• Implement multivariate statistical methods (e.g., PERMANOVA, ANOSIM)
• Analyze differential abundance using appropriate tools (e.g., DESeq2, ALDEx2)
• Identify significant taxa associated with specific environmental conditions or host plants
• Create publication-ready diversity figures