In ecology, alpha diversity (α-diversity) is the mean species diversity in sites or habitats at a local scale. The term was introduced by R. H. Whittaker together with the terms beta diversity (β-diversity) and gamma diversity (γ-diversity). Whittaker's idea was that the total species diversity in a landscape (gamma diversity) is determined by two different things, the mean species ...
Some commonly used indices to describe alpha diversity include Shannon' index (H), Simpson's index (D) and Renyi entropy. Beta diversity means the dissimilarity between communities of two sites ...
Alpha and beta diversity. Alpha diversity. Species richness (OTU count) "How many?" ... Species diversity (Shannon index) "How different?" How are the microbes balanced to each other? Do we have species evenness (similar abundance level) or do some species dominate others? Shannon index measures how evenly the microbes are distributed in a sample.
Alpha diversity graphics Examples using the plot_richness function. Although the function name includes the word richness , which usually refers to the total number of species/OTUs/taxa in a sample or environment – either observed or estimated – this is actually a wrapper for all descriptions of alpha diversity .
There are many measures of alpha diversity. Depending on your ecological allegiances, you may have a preference for Chao1, Simpson's Diversity, Shannon Index, etc.These all measure different things, so it's important to think about what is most meaningful for your experiment, and your question.
Note. There are different ways that samples are represented in the ecological literature and in related software. The alpha diversity measures provided here always assume that the input contains abundance data: each count represents the number of individuals seen for a particular OTU in the sample. For example, if you have two OTUs, where 3 individuals were observed from one of the OTUs and ...
alpha_diversity.py – Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics¶. Description: This script calculates alpha diversity, or within-sample diversity, using an OTU table. The QIIME pipeline allows users to conveniently calculate more than two dozen different diversity metrics.
The terms alpha, beta, and gamma diversity were all introduced by R. H. Whittaker to describe the spatial component of biodiversity. Imagine that you have a landscape containing of a number of separate sites and habitats. Alpha diversity is just the diversity of each site (local species pool).Beta diversity represents the differences in species composition among sites.
Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. ... Shannon’s diversity (H’), Simpson’s diversity (D 1), ... Jost L. Partitioning diversity into independent alpha and beta components. Ecology. 2007; 88:2427–2439.
A diversity index is a quantitative measure that reflects how many different types (such as species) there are in a dataset (a community), and simultaneously takes into account how evenly the basic entities (such as individuals) are distributed among those types.. When diversity indices are used in ecology, the types of interest are usually species, but they can also be other categories, such ...