Ecological Diversity Analysis Across Five Sites Using R

 Introduction

Biodiversity is a cornerstone of ecological research and conservation. Quantifying biodiversity using ecological indices provides insight into species distribution, abundance, and dominance within habitats. Commonly used indices include:

• Species Richness: the total number of different species.
• Shannon Index: accounts for both abundance and evenness.
• Simpson Index: measures the probability that two individuals randomly selected belong to the same species.
• Evenness: how evenly individuals are distributed across species.
• Berger-Parker Index: indicates species dominance by focusing on the most abundant species.

The goal of this analysis is to assess and compare biodiversity across five sites (Site_A to Site_E) using these indices.

Materials and Methods

Study Area

Five sites, labeled Site_A through Site_E, were sampled for biodiversity data. The dataset includes species counts, from which diversity indices were computed.

Software Used

• R (version 4.x) with packages like vegan, ggplot2, and pheatmap.

Indices Calculated

The following indices were calculated using the vegan package in R:

• Richness (S): Total number of species per site.
• Shannon Index (H′): $H′ = -\sum (p_i \cdot \ln p_i)$
  

Visualization

• Bar plot for index comparison across sites.
• Heatmap with hierarchical clustering to visualize similarity among sites based on index values.

Results

1. Result Table Interpretation

The table below shows five diversity indices (Richness, Shannon, Simpson, Evenness, and Berger-Parker) across five sites:

Site	Richness	Shannon	Simpson	Evenness	Berger-Parker
Site_A	23	2.931	0.939	0.935	0.117
Site_B	22	2.906	0.938	0.940	0.106
Site_C	24	3.019	0.946	0.950	0.092
Site_D	23	2.957	0.942	0.943	0.091
Site_E	23	2.921	0.937	0.931	0.112

Explanation of Each Index:

• Richness (S): Site_C (24) > others, suggesting it supports the highest species count.
• Shannon Index (H′): Highest at Site_C (3.019), reflecting both richness and equitable distribution.
• Simpson Index (1-D): Close across sites; Site_C highest (0.946) shows greater probability of selecting different species.
• Evenness (E): Nearly uniform (0.931–0.950); Site_C slightly more even in species distribution.
• Berger-Parker Index: Measures species dominance; lower values indicate higher diversity. Site_D (0.091) has least dominance, followed closely by Site_C (0.092).

Summary: Site_C is consistently the most diverse across all indices, while Site_B shows relatively lower diversity.

2. Bar Plot Interpretation

Figure Title: Comparison of Diversity Indices Across Sites

The bar plot is arranged into five panels, each representing one diversity index. Within each panel, bars for all five sites are compared visually.

Panel 1: Richness

• Site_C has the highest Richness (24), suggesting the richest habitat.
• Site_B shows the lowest (22), indicating fewer species.

Panel 2: Shannon Index

• Again, Site_C stands out (3.02), implying high diversity and balanced species abundance.
• Site_B is slightly lower (2.91), indicating lower entropy in species distribution.

Panel 3: Simpson Index

•     Small variations (0.937–0.946), but Site_C leads with the highest diversity.
•     All sites are quite similar, reflecting overall biodiversity health.

 Panel 4: Evenness

•     Site_C (0.950) is the most even, showing species are evenly distributed.
•     Site_E has the lowest evenness (0.931), indicating some species may be more dominant.

Panel 5: Berger-Parker Index

•     Site_D (0.091) and Site_C (0.092) show the least dominance of any single species.
•     Site_A (0.117) has the highest dominance, meaning one species is more abundant.

Visual Insight: The plot visually reinforces that Site_C consistently performs better in all diversity measures, indicating a well-balanced ecosystem.

3. Heatmap Interpretation

Figure Title: Heatmap of Diversity Indices

This clustered heatmap presents a tabular view of index values, color-coded for intensity, and hierarchically groups sites based on their similarity.

Color Gradient:

•     Dark Blue: High values (especially for Richness).
•     Pale Yellow: Lower values.
•     Interpretation: The heatmap visually compares relative performance across indices and sites.

Hierarchical Clustering:

•     Dendrogram shows Site_C and Site_D are most similar.
•     Site_A, Site_B, and Site_E are grouped separately, indicating different diversity patterns.

Visual Summary: The clustering confirms Site_C and Site_D are the most ecologically similar and most diverse, while Site_B and Site_E are relatively less diverse.

 Summary Points:

• Site_C leads in all metrics: Richness, Shannon, Simpson, Evenness, and lowest Berger-Parker (low dominance).
• Site_D is a close second in diversity and shows lowest dominance.
• Site_B shows the lowest species richness and Shannon index.
• Clustering validates these patterns and groups sites with similar diversity profiles.

Conclusion

This ecological diversity analysis using R software demonstrates Site_C as the most ecologically diverse among the five surveyed locations. The combination of bar plots and heatmaps offers a clear comparative view. These insights are crucial for ecological monitoring, habitat management, and biodiversity conservation planning.

Future studies could incorporate temporal data, beta diversity, and taxonomic composition to deepen ecological interpretations.