Question

What is alpha diversity?

Answer 1

Alpha diversity:

1. The mean diversity of a species in different habitats on a small scale is termed alpha diversity.
2. Alpha diversity is represented by showing the number of species in a particular ecosystem which is referred to as species richness.
3. Species richness: Number of species or operational taxonomic units (OTU) in a given area or ecosystem.
4. R.H Whittaker coined three terms alpha, beta, and gamma diversities.

Common types of alpha diversity indices are:

Chao Index:

1. There are two types of Chao Index, Chao1 and Chao2. Chao1 is an estimator based on abundance.
2. Therefore, we need data related to the frequency of individual samples that belong to a particular class.
3. Chao2, on the other hand, is an estimator based on the incidence.

Simpson Index:

1. The Simpson Index is a measure of the level of concentration when classifying people into types.
2. It was introduced by Edward H. Simpson in 1949.

Shannon Index:

1. Also known as the Shannon Diversity Index or Shannon Entropy, the Shannon Index is one of the most popular diversity indexes in the ecology literature.
2. The idea of ​​this metric is that the clearer the string and the equal proportions of the strings in question, the harder it is to predict the next character in the string.

ACE Index:

1. The ACE (Abundance Based Coverage Estimators) index is a diversity metric containing arbitrary abundance thresholds for labeling S_abun as the number of common taxa and S_rare as the number of rare taxa.

Good's Coverage Ind:

1. The Good`s Coverage Index is another alpha diversity estimator calculated by the following formula.
2. Use and type of Alpha Diversity metric in microbial NGS.
3. Where F1 is the number of singleton OTUs, N is the total number of individuals, or total is all OTUs.