Alpha Diversity

What is alpha diversity?

Alpha Diversity examines the microbial composition within a single sample. It considers two major questions related to species richness and species diversity:

Species richness: How many microbes are in a sample?

Simply, this is a count of different taxa found within a sample.

A sample high in species richness has a relatively high number of species present and vice versa.

Species diversity: How are the microbes balanced with each other in the sample?

Simply, this describes the relative proportions of taxa within a sample.

A sample with a high species diversity index would have many species of similar abundances (evenness). Alternatively, if one or a few species were dominant, this would produce a lower species diversity value.

Alpha Diversity Analyses

Alpha Diversity within each sample can be compared between samples, by comparing each sample’s indices. Different population distributions and metadata factors may lead to confounding results. However, normally-distributed populations and other distributions can be accounted for using t-tests and Mann-Whitney tests, respectively. Sample factors that should be listed in the metadata can be considered with linear modelling.

There are multiple formulae to calculate these indices (Shannon, Simpson, Chao1, etc.) Navigate through the definitions below to find out more.

Pairwise Wilcoxon Tests

Pairwise Wilcoxon tests, also known as Wilcoxon rank-sum tests or Mann-Whitney U tests, are non-parametric statistical tests used to determine whether two independent samples come from populations with the same distribution. These tests are often applied when the data is not normally distributed or when the assumption of equal variances is violated.

Observed OTUs

In microbiology and ecology, OTU stands for ‘Operational Taxonomic Unit.’ It is a way to define and group similar sequences of DNA, often used for the analysis of microbial diversity in environmental samples. ‘Observed OTUs’ refer to the actual number of unique OTUs that have been identified or counted in a given sample. It provides a measure of species or taxonomic richness in a sample.

ACE (Abundance-based Coverage Estimator)

ACE is a statistical method used in biodiversity and ecology to estimate species richness in a community or ecosystem. It is based on the abundance of species and estimates the number of additional species that are likely to be present but have not been observed. ACE is commonly used in microbial ecology and other fields to assess the diversity of microorganisms.

Berger-Parker Index (d)

The Berger-Parker Index is a simple measure of biodiversity that quantifies the dominance of the most abundant species in a community. It is calculated by taking the proportion of individuals belonging to the most abundant species in a sample. The index ranges from 0 (when all species are equally abundant) to 1 (when one species completely dominates the sample).

Fisher’s Alpha

Fisher’s Alpha is a diversity index commonly used in ecology to quantify species diversity within a community. It takes into account both the number of species (species richness) and the evenness of their distribution. Fisher’s Alpha is often used when the species-abundance distribution follows a log-series distribution. It is a parameter used to describe the shape of this distribution and can be used to compare diversity between different communities.

Chao1 (Chao’s Richness Estimator)

Chao1 is a statistical estimator used to estimate the true number of species (species richness) in a community or sample, especially when some species are rare and may not be observed in the sample. It takes into account both the number of observed species and the number of rare or singleton species to provide an estimate of total species richness.

Simpson Index (D)

The Simpson Index is a measure of diversity that quantifies the probability that two randomly selected individuals from a community belong to the same species. It ranges from 0 to 1, with higher values indicating lower diversity. It is often used to assess the dominance of a few abundant species in a community.

Simpson’s Evenness (E)

Simpson’s Evenness, often denoted as ‘E,’ is a measure that complements the Simpson Index. It quantifies how evenly the individuals are distributed among the different species in a community. A high evenness value indicates that species are equally represented, while a low value suggests that a few species dominate.

Shannon Equitability

Shannon Equitability is a measure of species evenness in a community. It is calculated by dividing the Shannon Diversity Index by the maximum possible Shannon Diversity Index for a given number of species. It provides a normalized measure of diversity, allowing for comparisons of evenness between communities with different numbers of species.

Shannon Diversity Index (H or H’)

The Shannon Diversity Index, often denoted as ‘H’ or ‘H’,’ is a widely used measure of biodiversity. It takes into account both species richness and species evenness. It is calculated based on the logarithm of the relative abundances of species in a community. Higher values of Shannon Diversity indicate higher species richness and evenness.

Inverse Simpson Index

The Inverse Simpson Index is another measure of diversity that focuses on species richness and evenness. It is the reciprocal of the Simpson Index and is often used to emphasize the importance of rare species in a community. Higher values indicate greater diversity.